From 1a0140269356f91d4b2f5050fb6a4ad562a14ad0 Mon Sep 17 00:00:00 2001 From: John Huddleston Date: Fri, 15 Dec 2023 15:38:36 -0800 Subject: [PATCH 1/3] Add Welsh et al. epitope sites and escape scores Adds distance maps for epitope sites and average escape scores based on antigenic escape scores from Welsh et al. 2023 [1], adds these maps to the distance maps config, and only exposes these distances through the nextflu-private builds Auspice config JSON for now. Adds the Python notebook used to generate these distance maps from the original raw data, so we can rebuild them later as needed. [1] https://www.biorxiv.org/content/10.1101/2023.12.12.571235v1 --- config/distance_maps.tsv | 2 + .../h3n2/ha/welsh_epitope_sites.json | 21 + .../welsh_escape_by_site_and_amino_acid.json | 8340 +++++++++++++++++ ...tes-and-scores-from-Welsh-et-al-data.ipynb | 585 ++ .../h3n2/ha/auspice_config.json | 10 + 5 files changed, 8958 insertions(+) create mode 100644 config/distance_maps/h3n2/ha/welsh_epitope_sites.json create mode 100644 config/distance_maps/h3n2/ha/welsh_escape_by_site_and_amino_acid.json create mode 100644 notebooks/2023-12-15-identify-epitope-sites-and-scores-from-Welsh-et-al-data.ipynb diff --git a/config/distance_maps.tsv b/config/distance_maps.tsv index 18f4b8d0..ab3c961e 100644 --- a/config/distance_maps.tsv +++ b/config/distance_maps.tsv @@ -3,6 +3,8 @@ h3n2 ha root ep wolf h3n2 ha root ne wolf_nonepitope h3n2 ha root rb koel h3n2 ha ancestor ne_star luksza_nonepitope +h3n2 ha root welsh_ep welsh_epitope_sites +h3n2 ha root welsh_escape welsh_escape_by_site_and_amino_acid h3n2 na root ep bhatt h3n2 na root ne bhatt_nonepitope h1n1pdm ha root ep canton diff --git a/config/distance_maps/h3n2/ha/welsh_epitope_sites.json b/config/distance_maps/h3n2/ha/welsh_epitope_sites.json new file mode 100644 index 00000000..e8f0b360 --- /dev/null +++ b/config/distance_maps/h3n2/ha/welsh_epitope_sites.json @@ -0,0 +1,21 @@ +{ + "name": "Welsh et al. epitope sites", + "default": 0, + "map": { + "HA1": { + "50": 1, + "82": 1, + "124": 1, + "135": 1, + "143": 1, + "144": 1, + "145": 1, + "157": 1, + "159": 1, + "189": 1, + "193": 1, + "275": 1, + "276": 1 + } + } +} \ No newline at end of file diff --git a/config/distance_maps/h3n2/ha/welsh_escape_by_site_and_amino_acid.json b/config/distance_maps/h3n2/ha/welsh_escape_by_site_and_amino_acid.json new file mode 100644 index 00000000..fbc5e16a --- /dev/null +++ b/config/distance_maps/h3n2/ha/welsh_escape_by_site_and_amino_acid.json @@ -0,0 +1,8340 @@ +{ + "name": "Welsh et al. escape scores 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+ } +} \ No newline at end of file diff --git a/notebooks/2023-12-15-identify-epitope-sites-and-scores-from-Welsh-et-al-data.ipynb b/notebooks/2023-12-15-identify-epitope-sites-and-scores-from-Welsh-et-al-data.ipynb new file mode 100644 index 00000000..ee9321b0 --- /dev/null +++ b/notebooks/2023-12-15-identify-epitope-sites-and-scores-from-Welsh-et-al-data.ipynb @@ -0,0 +1,585 @@ +{ + "cells": [ + { + "cell_type": "markdown", + "id": "9cb97707-6a2b-45d6-bdff-f7c8431867fd", + "metadata": {}, + "source": [ + "# Identify H3N2 epitope sites and average escape scores from antigenic escape scores per serum, site, and amino acid\n", + "\n", + "Identifies contemporary epitope sites and average escape scores from experimental measurements. Antigenic escape scores were originally calculated in Welsh et al. 2023 per serum a range of age groups. In this notebook, we identify putative antigenic sites or \"epitope sites\" where mutations should allow recent H3N2 strains to escape existing immunity. These sites augment the historical epitope sites from Wolf et al. 2006 that Nextstrain seasonal influenza analyses use to calculate \"epitope mutations\" in each HA tree.\n", + "\n", + "In addition to finding epitope sites from experimental data, we also calculate the average non-negative antigenic escape score per HA1 site/position and amino acid mutation from the wildtype. We save these average scores as [an Augur \"distance map\"](https://docs.nextstrain.org/projects/augur/en/stable/usage/cli/distance.html) which allows us to calculate a cumulative escape score for all HA1 amino acid mutations per strain in a given HA tree. We use non-negative escape scores to reflect the assumption that mutations with negative escape scores are less likely to occur in nature." + ] + }, + { + "cell_type": "markdown", + "id": "157ca5b1-e6d4-4a7c-94c5-52a9b5eed9e4", + "metadata": {}, + "source": [ + "## Import" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "582c5ab8-08e4-40e5-89f4-10cf1d1cb915", + "metadata": {}, + "outputs": [], + "source": [ + "import json\n", + "import pandas as pd" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "6cb7a594-74e6-4796-a701-7af4b0f668ab", + "metadata": {}, + "outputs": [], + "source": [ + "ha1_amino_acids = 329" + ] + }, + { + "cell_type": "markdown", + "id": "780c349b-45a7-4987-8cbd-21fd400fceb2", + "metadata": {}, + "source": [ + "Define the number of standard deviations from the mean to use for the threshold of putative epitope sites." + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "fd05229c-5cb6-478b-9aaf-567a9b239873", + "metadata": {}, + "outputs": [], + "source": [ + "n_std_dev = 4" + ] + }, + { + "cell_type": "markdown", + "id": "232f1256-31a5-466e-91f0-a93a979cc2d4", + "metadata": {}, + "source": [ + "## Load data" + ] + }, + { + "cell_type": "markdown", + "id": "b858d938-e145-44f0-9397-8bde768219f3", + "metadata": {}, + "source": [ + "Load data from the merged and filtered escape scores in [the Welsh et al. GitHub repository](https://github.com/dms-vep/flu_h3_hk19_dms.git)." + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "0934f0eb-e6e1-4da2-9c58-94fc348b3099", + "metadata": {}, + "outputs": [], + "source": [ + "escape_scores = pd.read_csv(\"https://github.com/dms-vep/flu_h3_hk19_dms/raw/main/results/full_hk19_escape_scores.csv\")" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "4ded5f2e-5e97-48dd-9c3f-cf574042a61b", + "metadata": {}, + "outputs": [], + "source": [ + "escape_scores.shape" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "5a6630ab-17ce-40d1-9ba5-1499ca9e85c9", + "metadata": {}, + "outputs": [], + "source": [ + "escape_scores.head()" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "079bfb60-524e-49fc-91d4-12dd798e9ee4", + "metadata": {}, + "outputs": [], + "source": [ + "escape_scores[\"serum\"].drop_duplicates().shape" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "5597d582-27da-4d70-950f-1051d6cdf483", + "metadata": {}, + "outputs": [], + "source": [ + "set(escape_scores[\"serum\"].drop_duplicates().values)" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "8b26c159-7f8c-4781-86e1-be1df0b63887", + "metadata": {}, + "outputs": [], + "source": [ + "nonnegative_ha1_escape_scores = escape_scores.query(f\"(escape_mean >= 0) & (site > 0) & (site <= {ha1_amino_acids})\").copy()" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "b3c43d3e-d9b8-4840-a00a-4c7992610a90", + "metadata": {}, + "outputs": [], + "source": [ + "nonnegative_ha1_escape_scores.shape" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "5023a615-f7c9-49d2-90f5-f30b221a2a18", + "metadata": {}, + "outputs": [], + "source": [ + "nonnegative_ha1_escape_scores.head()" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "46e844c8-12e5-4be9-9471-9dcce555f861", + "metadata": {}, + "outputs": [], + "source": [ + "nonnegative_ha1_escape_scores.tail()" + ] + }, + { + "cell_type": "markdown", + "id": "dfc32eda-32b9-4fb6-aea2-b074a09b2831", + "metadata": {}, + "source": [ + "Sum non-negative escape scores per serum and site, calculate the mean and std dev, and identify putative epitope sites as those where the total escape score is greater than the mean plus 4 standard deviations." + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "65286fa0-6742-4428-9ced-5f40c7b207a2", + "metadata": {}, + "outputs": [], + "source": [ + "ha1_effects_per_serum_and_site = nonnegative_ha1_escape_scores.groupby([\n", + " \"serum\",\n", + " \"cohort\",\n", + " \"site\",\n", + "])[\"escape_mean\"].sum().reset_index().rename(columns={\"escape_mean\": \"escape_total\"})" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "c5e29308-de87-45e4-8fc7-610ddd94377c", + "metadata": {}, + "outputs": [], + "source": [ + "ha1_effects_per_serum_and_site.shape" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "486658b8-05e4-4a17-9cd3-4f88599cf6e1", + "metadata": {}, + "outputs": [], + "source": [ + "ha1_effects_per_serum_and_site.head()" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "56306afd-eed9-40ce-bf65-4135e1bc370c", + "metadata": {}, + "outputs": [], + "source": [ + "ha1_effects_per_serum = ha1_effects_per_serum_and_site.groupby(\n", + " \"serum\"\n", + ").agg({\n", + " \"escape_total\": [\"mean\", \"std\"]\n", + "}).reset_index().set_axis([\"serum\", \"serum_mean_escape_total\", \"serum_std_escape_total\"], axis=1)" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "f4e33cea-d555-4dc9-928a-a643d3958283", + "metadata": {}, + "outputs": [], + "source": [ + "ha1_effects_per_serum.shape" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "16d853ff-12fb-4968-9f76-85b0d8f13df9", + "metadata": {}, + "outputs": [], + "source": [ + "ha1_effects_per_serum.head()" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "03ef83b3-4184-4dac-aef9-e4b6769c1c43", + "metadata": {}, + "outputs": [], + "source": [ + "ha1_effects_per_serum[\"serum_escape_threshold\"] = (\n", + " ha1_effects_per_serum[\"serum_mean_escape_total\"] + (n_std_dev * ha1_effects_per_serum[\"serum_std_escape_total\"])\n", + ")" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "bff12db1-6320-4f82-bfd6-005c7843a6bb", + "metadata": {}, + "outputs": [], + "source": [ + "ha1_effects_per_serum.head()" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "1d657d5b-a380-45b6-8e7d-44f40be7766a", + "metadata": {}, + "outputs": [], + "source": [ + "ha1_effects_per_serum_and_site_with_threshold = ha1_effects_per_serum_and_site.merge(ha1_effects_per_serum, on=\"serum\")" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "76acd725-6a8c-4f89-816d-7917705e69fb", + "metadata": {}, + "outputs": [], + "source": [ + "ha1_effects_per_serum_and_site_with_threshold.head()" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "bedc64dc-77fd-43e3-a100-4d4528f0d761", + "metadata": {}, + "outputs": [], + "source": [ + "epitope_sites_by_serum = ha1_effects_per_serum_and_site_with_threshold.query(\"escape_total >= serum_escape_threshold\").copy()" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "951f7a14-6443-4ab7-b216-7246bf9a96a2", + "metadata": {}, + "outputs": [], + "source": [ + "epitope_sites_by_serum.head()" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "fac49d91-ee4e-4a9c-abea-0651d554dbc5", + "metadata": {}, + "outputs": [], + "source": [ + "epitope_site_counts = epitope_sites_by_serum.groupby(\"site\")[\"serum\"].count()" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "1005c53c-07d6-4d4b-b82e-2ced4b26dc8a", + "metadata": {}, + "outputs": [], + "source": [ + "epitope_site_counts" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "2f0ae520-7330-437e-a5b5-24d402b77a47", + "metadata": {}, + "outputs": [], + "source": [ + "epitope_sites = epitope_site_counts.index.values" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "b1d14b58-494e-4860-afbb-1450d252346d", + "metadata": {}, + "outputs": [], + "source": [ + "epitope_sites" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "095b93f0-3077-4483-89d5-cd127b14cdcd", + "metadata": {}, + "outputs": [], + "source": [ + "len(epitope_sites)" + ] + }, + { + "cell_type": "markdown", + "id": "a4a33e87-e4e1-444d-b835-0620a4715ed0", + "metadata": {}, + "source": [ + "Export a simple distance map for epitope sites where each site identified above has a weight of 1. When used with augur distance, this map calculates the Hamming distance between each sample and the MRCA of the tree at only these positions. All other mutations get ignored in that distance calculation." + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "cd1be7cd-567d-4a68-98a8-ee954dd2a76a", + "metadata": {}, + "outputs": [], + "source": [ + "epitope_site_distance_map = {\n", + " \"name\": \"Welsh et al. epitope sites\",\n", + " \"default\": 0,\n", + " \"map\": {\n", + " \"HA1\": {}\n", + " }\n", + "}" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "ef1d1297-883b-4fdc-bcfc-dae82a269336", + "metadata": {}, + "outputs": [], + "source": [ + "for site in epitope_sites:\n", + " epitope_site_distance_map[\"map\"][\"HA1\"][str(site)] = 1" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "987aa9a9-1d53-4923-b502-31d97e7c0d37", + "metadata": {}, + "outputs": [], + "source": [ + "epitope_site_distance_map" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "56ee1509-e582-4630-9ebf-89c74b1a0289", + "metadata": {}, + "outputs": [], + "source": [ + "with open(\"welsh_epitope_sites.json\", \"w\") as oh:\n", + " json.dump(\n", + " epitope_site_distance_map,\n", + " oh,\n", + " indent=2,\n", + " )" + ] + }, + { + "cell_type": "markdown", + "id": "dfcd184c-8250-4e6f-af6f-eb1123ed1098", + "metadata": {}, + "source": [ + "## Calculate average nonnegative scores per site and amino acid across all samples" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "0b28eaeb-9320-43ae-9953-f4863ec56b89", + "metadata": {}, + "outputs": [], + "source": [ + "total_score_per_site_and_amino_acid = {}" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "00008ce0-1cbf-4795-baab-e6dd7bbe30fa", + "metadata": {}, + "outputs": [], + "source": [ + "count_score_per_site_and_amino_acid = {}" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "49c37b70-5ee1-4812-a15a-ef3c1c146dce", + "metadata": {}, + "outputs": [], + "source": [ + "nonnegative_ha1_escape_scores.head()" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "e0c0dd00-485e-418f-8884-57105d5a66f4", + "metadata": {}, + "outputs": [], + "source": [ + "mean_escape_score_by_site_and_amino_acid = nonnegative_ha1_escape_scores.groupby([\n", + " \"site\",\n", + " \"wildtype\",\n", + " \"mutant\",\n", + "])[\"escape_mean\"].mean().to_dict()" + ] + }, + { + "cell_type": "markdown", + "id": "00c62c81-aa8c-41ad-b092-fb525eb1c2ed", + "metadata": {}, + "source": [ + "Export a per-site-and-amino-acid distance map for the average scores calculated above. When used with augur distance, this map will calculate a weighted Hamming distance between each sample and the MRCA of the tree at any site with a mutation specifically from the wild type allele to the experimentally measured allele. The weights of the Hamming distance are the average escape score values for each site and amino acid mutation." + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "3ab7eff8-8c81-4427-8eaf-2ecb91e45b4a", + "metadata": {}, + "outputs": [], + "source": [ + "distance_map = {\n", + " \"name\": \"Welsh et al. escape scores per site and amino acid\",\n", + " \"default\": 0,\n", + " \"map\": {\n", + " \"HA1\": {}\n", + " }\n", + "}" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "7640cc4a-1602-4ae8-88b8-54c5484ee2c6", + "metadata": {}, + "outputs": [], + "source": [ + "for (site, wildtype, mutant), escape_score in mean_escape_score_by_site_and_amino_acid.items():\n", + " if str(site) not in distance_map[\"map\"][\"HA1\"]:\n", + " distance_map[\"map\"][\"HA1\"][str(site)] = []\n", + "\n", + " distance_map[\"map\"][\"HA1\"][str(site)].append({\n", + " \"from\": wildtype,\n", + " \"to\": mutant,\n", + " \"weight\": round(escape_score, 6),\n", + " })" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "dc00fbb5-2daf-41ab-b123-28bb5d3bc00f", + "metadata": {}, + "outputs": [], + "source": [ + "distance_map[\"map\"][\"HA1\"][\"160\"]" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "e6194612-4401-4a23-a6c9-700aba4b3b5a", + "metadata": {}, + "outputs": [], + "source": [ + "distance_map[\"map\"][\"HA1\"][\"223\"]" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "248c9052-7238-4a7b-99dc-24f5bc234393", + "metadata": {}, + "outputs": [], + "source": [ + "distance_map[\"map\"][\"HA1\"][\"140\"]" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "f12d94ef-0124-4d91-b295-4fa89abd9e3b", + "metadata": {}, + "outputs": [], + "source": [ + "with open(\"welsh_escape_by_site_and_amino_acid.json\", \"w\") as oh:\n", + " json.dump(\n", + " distance_map,\n", + " oh,\n", + " indent=2,\n", + " )" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "10bb367b-ad31-43ca-afff-7226f59349a6", + "metadata": {}, + "outputs": [], + "source": [] + } + ], + "metadata": { + "kernelspec": { + "display_name": "Python 3 (ipykernel)", + "language": "python", + "name": "python3" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython3", + "version": "3.12.0" + } + }, + "nbformat": 4, + "nbformat_minor": 5 +} diff --git a/profiles/nextflu-private/h3n2/ha/auspice_config.json b/profiles/nextflu-private/h3n2/ha/auspice_config.json index 0fc7b40e..a17da0e3 100644 --- a/profiles/nextflu-private/h3n2/ha/auspice_config.json +++ b/profiles/nextflu-private/h3n2/ha/auspice_config.json @@ -171,6 +171,16 @@ "title": "RBS adjacent mutations", "type": "continuous" }, + { + "key": "welsh_ep", + "title": "Welsh et al. epitope mutations", + "type": "continuous" + }, + { + "key": "welsh_escape", + "title": "Welsh et al. escape score", + "type": "continuous" + }, { "key": "glyc", "title": "Glycosylation changes", From 60a3c407e1799771dcd94c8f41ef220a2f193421 Mon Sep 17 00:00:00 2001 From: John Huddleston Date: Mon, 18 Dec 2023 14:52:48 -0800 Subject: [PATCH 2/3] Update sites to reflect inclusion of 2 additional serum samples --- .../h3n2/ha/welsh_epitope_sites.json | 1 + .../welsh_escape_by_site_and_amino_acid.json | 1861 +++++++++-------- 2 files changed, 959 insertions(+), 903 deletions(-) diff --git a/config/distance_maps/h3n2/ha/welsh_epitope_sites.json b/config/distance_maps/h3n2/ha/welsh_epitope_sites.json index e8f0b360..9f3ae6f7 100644 --- a/config/distance_maps/h3n2/ha/welsh_epitope_sites.json +++ b/config/distance_maps/h3n2/ha/welsh_epitope_sites.json @@ -7,6 +7,7 @@ "82": 1, "124": 1, "135": 1, + "137": 1, "143": 1, "144": 1, "145": 1, diff --git a/config/distance_maps/h3n2/ha/welsh_escape_by_site_and_amino_acid.json b/config/distance_maps/h3n2/ha/welsh_escape_by_site_and_amino_acid.json index fbc5e16a..263826f4 100644 --- a/config/distance_maps/h3n2/ha/welsh_escape_by_site_and_amino_acid.json +++ b/config/distance_maps/h3n2/ha/welsh_escape_by_site_and_amino_acid.json @@ -12,31 +12,31 @@ { "from": "Q", "to": "R", - "weight": 0.064755 + "weight": 0.060408 } ], "2": [ { "from": "K", "to": "N", - "weight": 0.047108 + "weight": 0.050964 } ], "3": [ { "from": "I", "to": "A", - "weight": 0.048244 + "weight": 0.058464 }, { "from": "I", "to": "D", - "weight": 0.050621 + "weight": 0.05142 }, { "from": "I", "to": "E", - "weight": 0.025 + "weight": 0.02348 }, { "from": "I", @@ -56,7 +56,7 @@ { "from": "I", "to": "K", - "weight": 0.049755 + "weight": 0.060908 }, { "from": "I", @@ -71,12 +71,12 @@ { "from": "I", "to": "N", - "weight": 0.033388 + "weight": 0.031022 }, { "from": "I", "to": "P", - "weight": 0.02405 + "weight": 0.0327 }, { "from": "I", @@ -96,12 +96,12 @@ { "from": "I", "to": "V", - "weight": 0.033167 + "weight": 0.036627 }, { "from": "I", "to": "W", - "weight": 0.08365 + "weight": 0.079188 }, { "from": "I", @@ -118,12 +118,12 @@ { "from": "P", "to": "C", - "weight": 0.067743 + "weight": 0.054989 }, { "from": "P", "to": "D", - "weight": 0.056975 + "weight": 0.0639 }, { "from": "P", @@ -133,7 +133,7 @@ { "from": "P", "to": "F", - "weight": 0.036935 + "weight": 0.035233 }, { "from": "P", @@ -143,12 +143,12 @@ { "from": "P", "to": "H", - "weight": 0.028271 + "weight": 0.030025 }, { "from": "P", "to": "I", - "weight": 0.036915 + "weight": 0.03444 }, { "from": "P", @@ -158,22 +158,22 @@ { "from": "P", "to": "L", - "weight": 0.0424 + "weight": 0.0445 }, { "from": "P", "to": "M", - "weight": 0.06939 + "weight": 0.080708 }, { "from": "P", "to": "N", - "weight": 0.055109 + "weight": 0.054308 }, { "from": "P", "to": "Q", - "weight": 0.058371 + "weight": 0.057288 }, { "from": "P", @@ -183,27 +183,27 @@ { "from": "P", "to": "S", - "weight": 0.032857 + "weight": 0.029737 }, { "from": "P", "to": "T", - "weight": 0.037658 + "weight": 0.037246 }, { "from": "P", "to": "V", - "weight": 0.023318 + "weight": 0.032125 }, { "from": "P", "to": "W", - "weight": 0.054375 + "weight": 0.049733 }, { "from": "P", "to": "Y", - "weight": 0.050373 + "weight": 0.046969 } ], "5": [ @@ -215,7 +215,7 @@ { "from": "G", "to": "D", - "weight": 0.028775 + "weight": 0.028238 }, { "from": "G", @@ -225,22 +225,22 @@ { "from": "G", "to": "F", - "weight": 0.0627 + "weight": 0.06514 }, { "from": "G", "to": "H", - "weight": 0.0469 + "weight": 0.047725 }, { "from": "G", "to": "I", - "weight": 0.051142 + "weight": 0.047308 }, { "from": "G", "to": "L", - "weight": 0.03469 + "weight": 0.038036 }, { "from": "G", @@ -250,22 +250,22 @@ { "from": "G", "to": "N", - "weight": 0.04848 + "weight": 0.056745 }, { "from": "G", "to": "P", - "weight": 0.067212 + "weight": 0.066706 }, { "from": "G", "to": "Q", - "weight": 0.02882 + "weight": 0.026545 }, { "from": "G", "to": "R", - "weight": 0.021478 + "weight": 0.02314 }, { "from": "G", @@ -275,12 +275,12 @@ { "from": "G", "to": "T", - "weight": 0.05956 + "weight": 0.0511 }, { "from": "G", "to": "V", - "weight": 0.046157 + "weight": 0.041869 }, { "from": "G", @@ -302,22 +302,22 @@ { "from": "N", "to": "D", - "weight": 0.045791 + "weight": 0.0441 }, { "from": "N", "to": "E", - "weight": 0.0424 + "weight": 0.0541 }, { "from": "N", "to": "F", - "weight": 0.059215 + "weight": 0.058679 }, { "from": "N", "to": "G", - "weight": 0.054781 + "weight": 0.068929 }, { "from": "N", @@ -327,7 +327,7 @@ { "from": "N", "to": "I", - "weight": 0.04704 + "weight": 0.051359 }, { "from": "N", @@ -337,7 +337,7 @@ { "from": "N", "to": "L", - "weight": 0.047043 + "weight": 0.048787 }, { "from": "N", @@ -347,7 +347,7 @@ { "from": "N", "to": "P", - "weight": 0.043564 + "weight": 0.045523 }, { "from": "N", @@ -372,7 +372,7 @@ { "from": "N", "to": "V", - "weight": 0.031186 + "weight": 0.042053 }, { "from": "N", @@ -404,12 +404,12 @@ { "from": "D", "to": "G", - "weight": 0.028167 + "weight": 0.025814 }, { "from": "D", "to": "H", - "weight": 0.066433 + "weight": 0.0603 }, { "from": "D", @@ -429,7 +429,7 @@ { "from": "D", "to": "M", - "weight": 0.035888 + "weight": 0.056611 }, { "from": "D", @@ -439,7 +439,7 @@ { "from": "D", "to": "P", - "weight": 0.068111 + "weight": 0.06273 }, { "from": "D", @@ -454,7 +454,7 @@ { "from": "D", "to": "T", - "weight": 0.0359 + "weight": 0.038067 }, { "from": "D", @@ -471,82 +471,82 @@ { "from": "N", "to": "A", - "weight": 0.06802 + "weight": 0.064713 }, { "from": "N", "to": "C", - "weight": 0.0486 + "weight": 0.043733 }, { "from": "N", "to": "D", - "weight": 0.046823 + "weight": 0.044543 }, { "from": "N", "to": "E", - "weight": 0.046193 + "weight": 0.055806 }, { "from": "N", "to": "F", - "weight": 0.047911 + "weight": 0.05338 }, { "from": "N", "to": "G", - "weight": 0.04695 + "weight": 0.043918 }, { "from": "N", "to": "H", - "weight": 0.065605 + "weight": 0.07206 }, { "from": "N", "to": "I", - "weight": 0.027467 + "weight": 0.0289 }, { "from": "N", "to": "K", - "weight": 0.029238 + "weight": 0.034307 }, { "from": "N", "to": "L", - "weight": 0.067493 + "weight": 0.068287 }, { "from": "N", "to": "M", - "weight": 0.041225 + "weight": 0.037822 }, { "from": "N", "to": "P", - "weight": 0.04348 + "weight": 0.046691 }, { "from": "N", "to": "Q", - "weight": 0.054708 + "weight": 0.05215 }, { "from": "N", "to": "R", - "weight": 0.01852 + "weight": 0.061933 }, { "from": "N", "to": "S", - "weight": 0.058664 + "weight": 0.067585 }, { "from": "N", "to": "T", - "weight": 0.075008 + "weight": 0.072836 }, { "from": "N", @@ -561,14 +561,14 @@ { "from": "N", "to": "Y", - "weight": 0.04934 + "weight": 0.051082 } ], "9": [ { "from": "S", "to": "A", - "weight": 0.05454 + "weight": 0.0498 }, { "from": "S", @@ -593,27 +593,27 @@ { "from": "S", "to": "H", - "weight": 0.058607 + "weight": 0.057531 }, { "from": "S", "to": "I", - "weight": 0.036122 + "weight": 0.0341 }, { "from": "S", "to": "K", - "weight": 0.050467 + "weight": 0.046143 }, { "from": "S", "to": "L", - "weight": 0.040491 + "weight": 0.037158 }, { "from": "S", "to": "M", - "weight": 0.059158 + "weight": 0.055154 }, { "from": "S", @@ -623,7 +623,7 @@ { "from": "S", "to": "P", - "weight": 0.085723 + "weight": 0.089553 }, { "from": "S", @@ -638,17 +638,17 @@ { "from": "S", "to": "T", - "weight": 0.06382 + "weight": 0.059909 }, { "from": "S", "to": "V", - "weight": 0.055071 + "weight": 0.089575 }, { "from": "S", "to": "W", - "weight": 0.028243 + "weight": 0.026925 }, { "from": "S", @@ -660,7 +660,7 @@ { "from": "T", "to": "A", - "weight": 0.071182 + "weight": 0.068246 }, { "from": "T", @@ -680,27 +680,27 @@ { "from": "T", "to": "F", - "weight": 0.060231 + "weight": 0.058236 }, { "from": "T", "to": "G", - "weight": 0.04345 + "weight": 0.03986 }, { "from": "T", "to": "H", - "weight": 0.070447 + "weight": 0.068481 }, { "from": "T", "to": "I", - "weight": 0.046011 + "weight": 0.043773 }, { "from": "T", "to": "K", - "weight": 0.048133 + "weight": 0.0542 }, { "from": "T", @@ -720,12 +720,12 @@ { "from": "T", "to": "R", - "weight": 0.0454 + "weight": 0.057314 }, { "from": "T", "to": "V", - "weight": 0.047027 + "weight": 0.045492 }, { "from": "T", @@ -735,7 +735,7 @@ { "from": "T", "to": "Y", - "weight": 0.045258 + "weight": 0.042346 } ], "11": [ @@ -747,19 +747,19 @@ { "from": "A", "to": "T", - "weight": 0.046429 + "weight": 0.043916 }, { "from": "A", "to": "V", - "weight": 0.026867 + "weight": 0.039071 } ], "12": [ { "from": "T", "to": "E", - "weight": 0.117517 + "weight": 0.102271 }, { "from": "T", @@ -774,17 +774,17 @@ { "from": "T", "to": "M", - "weight": 0.05768 + "weight": 0.069325 }, { "from": "T", "to": "V", - "weight": 0.06118 + "weight": 0.056667 }, { "from": "T", "to": "W", - "weight": 0.067407 + "weight": 0.091975 }, { "from": "T", @@ -796,19 +796,19 @@ { "from": "L", "to": "I", - "weight": 0.042225 + "weight": 0.041111 } ], "15": [ { "from": "L", "to": "I", - "weight": 0.040219 + "weight": 0.043 }, { "from": "L", "to": "V", - "weight": 0.053757 + "weight": 0.065975 } ], "16": [ @@ -829,7 +829,7 @@ { "from": "H", "to": "I", - "weight": 0.0268 + "weight": 0.028109 }, { "from": "H", @@ -846,22 +846,22 @@ { "from": "A", "to": "N", - "weight": 0.023111 + "weight": 0.022455 }, { "from": "A", "to": "S", - "weight": 0.035025 + "weight": 0.039111 }, { "from": "A", "to": "T", - "weight": 0.043878 + "weight": 0.05491 }, { "from": "A", "to": "V", - "weight": 0.05176 + "weight": 0.046783 } ], "20": [ @@ -880,17 +880,17 @@ { "from": "P", "to": "A", - "weight": 0.059312 + "weight": 0.060544 }, { "from": "P", "to": "F", - "weight": 0.066675 + "weight": 0.06381 }, { "from": "P", "to": "G", - "weight": 0.0512 + "weight": 0.053786 }, { "from": "P", @@ -900,7 +900,7 @@ { "from": "P", "to": "I", - "weight": 0.080261 + "weight": 0.076737 }, { "from": "P", @@ -910,12 +910,12 @@ { "from": "P", "to": "L", - "weight": 0.0363 + "weight": 0.03314 }, { "from": "P", "to": "M", - "weight": 0.039569 + "weight": 0.04248 }, { "from": "P", @@ -925,22 +925,22 @@ { "from": "P", "to": "Q", - "weight": 0.026833 + "weight": 0.0413 }, { "from": "P", "to": "R", - "weight": 0.03868 + "weight": 0.038306 }, { "from": "P", "to": "S", - "weight": 0.061422 + "weight": 0.07113 }, { "from": "P", "to": "T", - "weight": 0.059406 + "weight": 0.057611 }, { "from": "P", @@ -950,19 +950,19 @@ { "from": "P", "to": "W", - "weight": 0.055438 + "weight": 0.105711 } ], "22": [ { "from": "N", "to": "A", - "weight": 0.051273 + "weight": 0.046915 }, { "from": "N", "to": "D", - "weight": 0.048386 + "weight": 0.043088 }, { "from": "N", @@ -987,7 +987,7 @@ { "from": "N", "to": "Q", - "weight": 0.06305 + "weight": 0.064856 }, { "from": "N", @@ -1007,34 +1007,34 @@ { "from": "N", "to": "Y", - "weight": 0.076757 + "weight": 0.075075 } ], "24": [ { "from": "T", "to": "A", - "weight": 0.052767 + "weight": 0.046571 }, { "from": "T", "to": "E", - "weight": 0.042486 + "weight": 0.0459 }, { "from": "T", "to": "F", - "weight": 0.087808 + "weight": 0.081262 }, { "from": "T", "to": "H", - "weight": 0.039718 + "weight": 0.039608 }, { "from": "T", "to": "I", - "weight": 0.025813 + "weight": 0.025756 }, { "from": "T", @@ -1044,7 +1044,7 @@ { "from": "T", "to": "M", - "weight": 0.044533 + "weight": 0.0389 }, { "from": "T", @@ -1054,19 +1054,19 @@ { "from": "T", "to": "V", - "weight": 0.043233 + "weight": 0.041493 }, { "from": "T", "to": "Y", - "weight": 0.067 + "weight": 0.063767 } ], "25": [ { "from": "I", "to": "F", - "weight": 0.07936 + "weight": 0.085741 }, { "from": "I", @@ -1076,12 +1076,12 @@ { "from": "I", "to": "K", - "weight": 0.051583 + "weight": 0.045886 }, { "from": "I", "to": "L", - "weight": 0.091353 + "weight": 0.088831 }, { "from": "I", @@ -1091,12 +1091,12 @@ { "from": "I", "to": "Q", - "weight": 0.045786 + "weight": 0.047862 }, { "from": "I", "to": "R", - "weight": 0.036411 + "weight": 0.037173 }, { "from": "I", @@ -1111,7 +1111,7 @@ { "from": "I", "to": "W", - "weight": 0.059369 + "weight": 0.057424 }, { "from": "I", @@ -1123,19 +1123,19 @@ { "from": "V", "to": "I", - "weight": 0.0602 + "weight": 0.0612 } ], "27": [ { "from": "K", "to": "A", - "weight": 0.0505 + "weight": 0.046 }, { "from": "K", "to": "H", - "weight": 0.027312 + "weight": 0.025789 }, { "from": "K", @@ -1150,12 +1150,12 @@ { "from": "K", "to": "Q", - "weight": 0.041155 + "weight": 0.045038 }, { "from": "K", "to": "R", - "weight": 0.039894 + "weight": 0.043872 }, { "from": "K", @@ -1165,7 +1165,7 @@ { "from": "K", "to": "T", - "weight": 0.0461 + "weight": 0.046729 } ], "28": [ @@ -1177,7 +1177,7 @@ { "from": "T", "to": "S", - "weight": 0.06402 + "weight": 0.061133 } ], "29": [ @@ -1216,7 +1216,7 @@ { "from": "T", "to": "H", - "weight": 0.0054 + "weight": 0.01165 }, { "from": "T", @@ -1226,17 +1226,17 @@ { "from": "T", "to": "K", - "weight": 0.0533 + "weight": 0.05649 }, { "from": "T", "to": "L", - "weight": 0.068144 + "weight": 0.0665 }, { "from": "T", "to": "M", - "weight": 0.052312 + "weight": 0.054389 }, { "from": "T", @@ -1246,12 +1246,12 @@ { "from": "T", "to": "Q", - "weight": 0.0546 + "weight": 0.047767 }, { "from": "T", "to": "R", - "weight": 0.058623 + "weight": 0.069307 }, { "from": "T", @@ -1261,7 +1261,7 @@ { "from": "T", "to": "V", - "weight": 0.047123 + "weight": 0.056864 }, { "from": "T", @@ -1273,7 +1273,7 @@ { "from": "N", "to": "A", - "weight": 0.030138 + "weight": 0.035878 }, { "from": "N", @@ -1283,12 +1283,12 @@ { "from": "N", "to": "D", - "weight": 0.055325 + "weight": 0.052822 }, { "from": "N", "to": "E", - "weight": 0.047393 + "weight": 0.04895 }, { "from": "N", @@ -1303,7 +1303,7 @@ { "from": "N", "to": "H", - "weight": 0.063262 + "weight": 0.067694 }, { "from": "N", @@ -1323,17 +1323,17 @@ { "from": "N", "to": "M", - "weight": 0.034893 + "weight": 0.052862 }, { "from": "N", "to": "Q", - "weight": 0.064617 + "weight": 0.063315 }, { "from": "N", "to": "R", - "weight": 0.05626 + "weight": 0.062973 }, { "from": "N", @@ -1343,7 +1343,7 @@ { "from": "N", "to": "T", - "weight": 0.04783 + "weight": 0.046855 }, { "from": "N", @@ -1358,7 +1358,7 @@ { "from": "N", "to": "Y", - "weight": 0.053567 + "weight": 0.05425 } ], "32": [ @@ -1370,12 +1370,12 @@ { "from": "D", "to": "E", - "weight": 0.035083 + "weight": 0.032777 }, { "from": "D", "to": "G", - "weight": 0.058286 + "weight": 0.056037 }, { "from": "D", @@ -1390,37 +1390,37 @@ { "from": "D", "to": "L", - "weight": 0.097233 + "weight": 0.077825 }, { "from": "D", "to": "M", - "weight": 0.0534 + "weight": 0.05085 }, { "from": "D", "to": "N", - "weight": 0.047267 + "weight": 0.040629 }, { "from": "D", "to": "P", - "weight": 0.037333 + "weight": 0.04065 }, { "from": "D", "to": "Q", - "weight": 0.039815 + "weight": 0.045093 }, { "from": "D", "to": "S", - "weight": 0.052544 + "weight": 0.06233 }, { "from": "D", "to": "T", - "weight": 0.072667 + "weight": 0.09565 }, { "from": "D", @@ -1442,12 +1442,12 @@ { "from": "R", "to": "E", - "weight": 0.044973 + "weight": 0.041765 }, { "from": "R", "to": "F", - "weight": 0.038408 + "weight": 0.036392 }, { "from": "R", @@ -1462,32 +1462,32 @@ { "from": "R", "to": "I", - "weight": 0.05945 + "weight": 0.056689 }, { "from": "R", "to": "K", - "weight": 0.042186 + "weight": 0.039493 }, { "from": "R", "to": "L", - "weight": 0.030038 + "weight": 0.037578 }, { "from": "R", "to": "M", - "weight": 0.040207 + "weight": 0.040576 }, { "from": "R", "to": "N", - "weight": 0.033487 + "weight": 0.041367 }, { "from": "R", "to": "Q", - "weight": 0.038933 + "weight": 0.039129 }, { "from": "R", @@ -1497,12 +1497,12 @@ { "from": "R", "to": "W", - "weight": 0.036046 + "weight": 0.035086 }, { "from": "R", "to": "Y", - "weight": 0.052354 + "weight": 0.052073 } ], "34": [ @@ -1514,7 +1514,7 @@ { "from": "I", "to": "L", - "weight": 0.020582 + "weight": 0.026517 }, { "from": "I", @@ -1524,12 +1524,12 @@ { "from": "I", "to": "Q", - "weight": 0.0601 + "weight": 0.054867 }, { "from": "I", "to": "T", - "weight": 0.020567 + "weight": 0.019671 }, { "from": "I", @@ -1541,7 +1541,7 @@ { "from": "E", "to": "A", - "weight": 0.01744 + "weight": 0.024814 }, { "from": "E", @@ -1551,12 +1551,12 @@ { "from": "E", "to": "Q", - "weight": 0.03868 + "weight": 0.036055 }, { "from": "E", "to": "S", - "weight": 0.073167 + "weight": 0.064043 } ], "37": [ @@ -1565,10 +1565,15 @@ "to": "I", "weight": 0.05612 }, + { + "from": "T", + "to": "M", + "weight": 0.0057 + }, { "from": "T", "to": "V", - "weight": 0.021575 + "weight": 0.01934 } ], "38": [ @@ -1580,17 +1585,22 @@ { "from": "N", "to": "C", - "weight": 0.05114 + "weight": 0.057883 }, { "from": "N", "to": "D", "weight": 0.0172 }, + { + "from": "N", + "to": "E", + "weight": 0.007 + }, { "from": "N", "to": "F", - "weight": 0.03936 + "weight": 0.0399 }, { "from": "N", @@ -1600,7 +1610,7 @@ { "from": "N", "to": "K", - "weight": 0.0197 + "weight": 0.1204 }, { "from": "N", @@ -1615,17 +1625,17 @@ { "from": "N", "to": "R", - "weight": 0.044614 + "weight": 0.053522 }, { "from": "N", "to": "S", - "weight": 0.034557 + "weight": 0.033787 }, { "from": "N", "to": "T", - "weight": 0.058 + "weight": 0.055817 }, { "from": "N", @@ -1637,14 +1647,14 @@ { "from": "A", "to": "S", - "weight": 0.061833 + "weight": 0.062571 } ], "40": [ { "from": "T", "to": "A", - "weight": 0.03285 + "weight": 0.0284 }, { "from": "T", @@ -1654,12 +1664,12 @@ { "from": "T", "to": "F", - "weight": 0.043775 + "weight": 0.04984 }, { "from": "T", "to": "I", - "weight": 0.08584 + "weight": 0.084991 }, { "from": "T", @@ -1669,22 +1679,22 @@ { "from": "T", "to": "M", - "weight": 0.022733 + "weight": 0.0756 }, { "from": "T", "to": "Q", - "weight": 0.05985 + "weight": 0.071333 }, { "from": "T", "to": "V", - "weight": 0.0224 + "weight": 0.02758 }, { "from": "T", "to": "Y", - "weight": 0.02965 + "weight": 0.021575 } ], "41": [ @@ -1698,27 +1708,27 @@ { "from": "Q", "to": "A", - "weight": 0.0486 + "weight": 0.04886 }, { "from": "Q", "to": "E", - "weight": 0.052981 + "weight": 0.056024 }, { "from": "Q", "to": "H", - "weight": 0.03965 + "weight": 0.046711 }, { "from": "Q", "to": "I", - "weight": 0.047693 + "weight": 0.048367 }, { "from": "Q", "to": "L", - "weight": 0.03963 + "weight": 0.039655 }, { "from": "Q", @@ -1728,12 +1738,12 @@ { "from": "Q", "to": "R", - "weight": 0.0143 + "weight": 0.025157 }, { "from": "Q", "to": "T", - "weight": 0.054278 + "weight": 0.05422 }, { "from": "Q", @@ -1743,14 +1753,14 @@ { "from": "Q", "to": "Y", - "weight": 0.041643 + "weight": 0.036575 } ], "45": [ { "from": "N", "to": "A", - "weight": 0.079164 + "weight": 0.076308 }, { "from": "N", @@ -1760,12 +1770,12 @@ { "from": "N", "to": "D", - "weight": 0.055667 + "weight": 0.04458 }, { "from": "N", "to": "G", - "weight": 0.048725 + "weight": 0.0654 }, { "from": "N", @@ -1775,27 +1785,27 @@ { "from": "N", "to": "I", - "weight": 0.036814 + "weight": 0.0465 }, { "from": "N", "to": "K", - "weight": 0.048778 + "weight": 0.04537 }, { "from": "N", "to": "L", - "weight": 0.04355 + "weight": 0.03788 }, { "from": "N", "to": "R", - "weight": 0.097978 + "weight": 0.09024 }, { "from": "N", "to": "S", - "weight": 0.070393 + "weight": 0.067153 }, { "from": "N", @@ -1812,17 +1822,17 @@ { "from": "S", "to": "A", - "weight": 0.056914 + "weight": 0.070563 }, { "from": "S", "to": "D", - "weight": 0.0457 + "weight": 0.0394 }, { "from": "S", "to": "E", - "weight": 0.042761 + "weight": 0.040716 }, { "from": "S", @@ -1842,12 +1852,12 @@ { "from": "S", "to": "I", - "weight": 0.034436 + "weight": 0.03545 }, { "from": "S", "to": "K", - "weight": 0.046443 + "weight": 0.060325 }, { "from": "S", @@ -1857,27 +1867,27 @@ { "from": "S", "to": "M", - "weight": 0.057625 + "weight": 0.063931 }, { "from": "S", "to": "N", - "weight": 0.02194 + "weight": 0.023533 }, { "from": "S", "to": "Q", - "weight": 0.046157 + "weight": 0.043173 }, { "from": "S", "to": "R", - "weight": 0.06668 + "weight": 0.077882 }, { "from": "S", "to": "T", - "weight": 0.050355 + "weight": 0.049808 }, { "from": "S", @@ -1887,12 +1897,12 @@ { "from": "S", "to": "W", - "weight": 0.04575 + "weight": 0.049283 }, { "from": "S", "to": "Y", - "weight": 0.047264 + "weight": 0.05625 } ], "47": [ @@ -1909,7 +1919,7 @@ { "from": "S", "to": "F", - "weight": 0.03685 + "weight": 0.041385 }, { "from": "S", @@ -1919,7 +1929,7 @@ { "from": "S", "to": "I", - "weight": 0.056322 + "weight": 0.0536 }, { "from": "S", @@ -1939,7 +1949,7 @@ { "from": "S", "to": "P", - "weight": 0.06023 + "weight": 0.068582 }, { "from": "S", @@ -1954,19 +1964,19 @@ { "from": "S", "to": "Y", - "weight": 0.041433 + "weight": 0.038614 } ], "48": [ { "from": "I", "to": "A", - "weight": 0.076489 + "weight": 0.078175 }, { "from": "I", "to": "D", - "weight": 0.083642 + "weight": 0.073021 }, { "from": "I", @@ -1976,7 +1986,7 @@ { "from": "I", "to": "F", - "weight": 0.080167 + "weight": 0.076269 }, { "from": "I", @@ -1986,17 +1996,17 @@ { "from": "I", "to": "H", - "weight": 0.056608 + "weight": 0.050714 }, { "from": "I", "to": "K", - "weight": 0.081888 + "weight": 0.07915 }, { "from": "I", "to": "L", - "weight": 0.056475 + "weight": 0.054872 }, { "from": "I", @@ -2006,27 +2016,27 @@ { "from": "I", "to": "N", - "weight": 0.049371 + "weight": 0.052127 }, { "from": "I", "to": "P", - "weight": 0.072353 + "weight": 0.090094 }, { "from": "I", "to": "Q", - "weight": 0.087022 + "weight": 0.08428 }, { "from": "I", "to": "R", - "weight": 0.112156 + "weight": 0.108189 }, { "from": "I", "to": "S", - "weight": 0.063507 + "weight": 0.061387 }, { "from": "I", @@ -2041,12 +2051,12 @@ { "from": "I", "to": "W", - "weight": 0.065132 + "weight": 0.067295 }, { "from": "I", "to": "Y", - "weight": 0.055371 + "weight": 0.06022 } ], "49": [ @@ -2058,7 +2068,7 @@ { "from": "G", "to": "P", - "weight": 0.076082 + "weight": 0.073333 }, { "from": "G", @@ -2075,52 +2085,52 @@ { "from": "E", "to": "A", - "weight": 0.10487 + "weight": 0.096367 }, { "from": "E", "to": "C", - "weight": 0.128435 + "weight": 0.123484 }, { "from": "E", "to": "F", - "weight": 0.118 + "weight": 0.112306 }, { "from": "E", "to": "H", - "weight": 0.132942 + "weight": 0.124492 }, { "from": "E", "to": "I", - "weight": 0.087612 + "weight": 0.082624 }, { "from": "E", "to": "K", - "weight": 0.117389 + "weight": 0.11679 }, { "from": "E", "to": "L", - "weight": 0.1153 + "weight": 0.108636 }, { "from": "E", "to": "M", - "weight": 0.141373 + "weight": 0.138282 }, { "from": "E", "to": "N", - "weight": 0.08775 + "weight": 0.0802 }, { "from": "E", "to": "P", - "weight": 0.101027 + "weight": 0.092608 }, { "from": "E", @@ -2130,7 +2140,7 @@ { "from": "E", "to": "R", - "weight": 0.134773 + "weight": 0.126475 }, { "from": "E", @@ -2140,12 +2150,12 @@ { "from": "E", "to": "T", - "weight": 0.107086 + "weight": 0.1032 }, { "from": "E", "to": "V", - "weight": 0.117009 + "weight": 0.1113 }, { "from": "E", @@ -2155,14 +2165,14 @@ { "from": "E", "to": "Y", - "weight": 0.093131 + "weight": 0.0906 } ], "51": [ { "from": "I", "to": "L", - "weight": 0.0737 + "weight": 0.073514 } ], "53": [ @@ -2179,7 +2189,7 @@ { "from": "D", "to": "G", - "weight": 0.0653 + "weight": 0.06243 }, { "from": "D", @@ -2189,12 +2199,12 @@ { "from": "D", "to": "Q", - "weight": 0.0761 + "weight": 0.085892 }, { "from": "D", "to": "S", - "weight": 0.08875 + "weight": 0.101264 } ], "54": [ @@ -2206,7 +2216,7 @@ { "from": "S", "to": "E", - "weight": 0.094526 + "weight": 0.10433 }, { "from": "S", @@ -2216,22 +2226,22 @@ { "from": "S", "to": "H", - "weight": 0.032793 + "weight": 0.0393 }, { "from": "S", "to": "K", - "weight": 0.056433 + "weight": 0.05362 }, { "from": "S", "to": "M", - "weight": 0.052229 + "weight": 0.052125 }, { "from": "S", "to": "N", - "weight": 0.03588 + "weight": 0.034882 }, { "from": "S", @@ -2241,12 +2251,12 @@ { "from": "S", "to": "R", - "weight": 0.026388 + "weight": 0.027433 }, { "from": "S", "to": "T", - "weight": 0.063689 + "weight": 0.06846 }, { "from": "S", @@ -2258,27 +2268,27 @@ { "from": "H", "to": "F", - "weight": 0.038382 + "weight": 0.046285 }, { "from": "H", "to": "I", - "weight": 0.06201 + "weight": 0.061317 }, { "from": "H", "to": "L", - "weight": 0.047167 + "weight": 0.04596 }, { "from": "H", "to": "W", - "weight": 0.08 + "weight": 0.07211 }, { "from": "H", "to": "Y", - "weight": 0.051838 + "weight": 0.047933 } ], "57": [ @@ -2295,7 +2305,7 @@ { "from": "Q", "to": "E", - "weight": 0.049555 + "weight": 0.054433 }, { "from": "Q", @@ -2305,12 +2315,12 @@ { "from": "Q", "to": "H", - "weight": 0.016078 + "weight": 0.01965 }, { "from": "Q", "to": "I", - "weight": 0.043036 + "weight": 0.039658 }, { "from": "Q", @@ -2320,44 +2330,44 @@ { "from": "Q", "to": "L", - "weight": 0.03758 + "weight": 0.035244 }, { "from": "Q", "to": "M", - "weight": 0.046575 + "weight": 0.04042 }, { "from": "Q", "to": "N", - "weight": 0.04158 + "weight": 0.05209 }, { "from": "Q", "to": "R", - "weight": 0.038067 + "weight": 0.0403 }, { "from": "Q", "to": "S", - "weight": 0.042627 + "weight": 0.041065 }, { "from": "Q", "to": "T", - "weight": 0.0245 + "weight": 0.05846 }, { "from": "Q", "to": "V", - "weight": 0.075354 + "weight": 0.070871 } ], "58": [ { "from": "I", "to": "V", - "weight": 0.050828 + "weight": 0.054163 } ], "59": [ @@ -2386,7 +2396,7 @@ { "from": "G", "to": "E", - "weight": 0.047842 + "weight": 0.05043 }, { "from": "G", @@ -2401,17 +2411,17 @@ { "from": "G", "to": "K", - "weight": 0.073325 + "weight": 0.068069 }, { "from": "G", "to": "L", - "weight": 0.022089 + "weight": 0.02673 }, { "from": "G", "to": "M", - "weight": 0.047767 + "weight": 0.0466 }, { "from": "G", @@ -2493,7 +2503,7 @@ { "from": "Q", "to": "H", - "weight": 0.0556 + "weight": 0.0591 }, { "from": "Q", @@ -2530,46 +2540,46 @@ { "from": "D", "to": "E", - "weight": 0.0303 + "weight": 0.045425 } ], "78": [ { "from": "G", "to": "C", - "weight": 0.068158 + "weight": 0.070954 }, { "from": "G", "to": "D", - "weight": 0.072038 + "weight": 0.072195 }, { "from": "G", "to": "E", - "weight": 0.052894 + "weight": 0.057455 }, { "from": "G", "to": "S", - "weight": 0.04456 + "weight": 0.042194 }, { "from": "G", "to": "V", - "weight": 0.02999 + "weight": 0.043991 } ], "79": [ { "from": "F", "to": "I", - "weight": 0.047159 + "weight": 0.053017 }, { "from": "F", "to": "L", - "weight": 0.062506 + "weight": 0.066568 } ], "80": [ @@ -2581,7 +2591,7 @@ { "from": "Q", "to": "E", - "weight": 0.059352 + "weight": 0.058348 }, { "from": "Q", @@ -2591,7 +2601,7 @@ { "from": "Q", "to": "M", - "weight": 0.021091 + "weight": 0.032358 }, { "from": "Q", @@ -2603,7 +2613,7 @@ { "from": "N", "to": "D", - "weight": 0.0372 + "weight": 0.03594 }, { "from": "N", @@ -2615,7 +2625,7 @@ { "from": "K", "to": "A", - "weight": 0.085004 + "weight": 0.087681 }, { "from": "K", @@ -2625,32 +2635,32 @@ { "from": "K", "to": "N", - "weight": 0.04025 + "weight": 0.04485 }, { "from": "K", "to": "Q", - "weight": 0.069111 + "weight": 0.066385 }, { "from": "K", "to": "R", - "weight": 0.042153 + "weight": 0.050806 }, { "from": "K", "to": "S", - "weight": 0.079808 + "weight": 0.096353 }, { "from": "K", "to": "T", - "weight": 0.072508 + "weight": 0.069646 }, { "from": "K", "to": "V", - "weight": 0.060878 + "weight": 0.061413 } ], "83": [ @@ -2662,7 +2672,7 @@ { "from": "K", "to": "D", - "weight": 0.062687 + "weight": 0.057944 }, { "from": "K", @@ -2672,47 +2682,47 @@ { "from": "K", "to": "H", - "weight": 0.047308 + "weight": 0.044677 }, { "from": "K", "to": "I", - "weight": 0.057887 + "weight": 0.067044 }, { "from": "K", "to": "M", - "weight": 0.08995 + "weight": 0.077757 }, { "from": "K", "to": "N", - "weight": 0.031621 + "weight": 0.035733 }, { "from": "K", "to": "Q", - "weight": 0.03335 + "weight": 0.037143 }, { "from": "K", "to": "R", - "weight": 0.036889 + "weight": 0.03344 }, { "from": "K", "to": "S", - "weight": 0.085915 + "weight": 0.089 }, { "from": "K", "to": "T", - "weight": 0.075367 + "weight": 0.072541 }, { "from": "K", "to": "V", - "weight": 0.050871 + "weight": 0.054853 }, { "from": "K", @@ -2722,14 +2732,14 @@ { "from": "K", "to": "Y", - "weight": 0.077915 + "weight": 0.083353 } ], "84": [ { "from": "W", "to": "F", - "weight": 0.0318 + "weight": 0.025125 } ], "86": [ @@ -2741,43 +2751,43 @@ { "from": "L", "to": "V", - "weight": 0.0334 + "weight": 0.031883 } ], "87": [ { "from": "F", "to": "Y", - "weight": 0.04799 + "weight": 0.046564 } ], "88": [ { "from": "V", "to": "I", - "weight": 0.04091 + "weight": 0.039962 }, { "from": "V", "to": "L", - "weight": 0.027667 + "weight": 0.056986 } ], "91": [ { "from": "S", "to": "E", - "weight": 0.100087 + "weight": 0.092922 }, { "from": "S", "to": "N", - "weight": 0.05308 + "weight": 0.070575 }, { "from": "S", "to": "P", - "weight": 0.0535 + "weight": 0.048154 }, { "from": "S", @@ -2787,34 +2797,34 @@ { "from": "S", "to": "T", - "weight": 0.022515 + "weight": 0.021064 } ], "92": [ { "from": "R", "to": "A", - "weight": 0.0446 + "weight": 0.052067 }, { "from": "R", "to": "C", - "weight": 0.10375 + "weight": 0.092756 }, { "from": "R", "to": "D", - "weight": 0.0522 + "weight": 0.050864 }, { "from": "R", "to": "E", - "weight": 0.036733 + "weight": 0.045846 }, { "from": "R", "to": "F", - "weight": 0.0341 + "weight": 0.035761 }, { "from": "R", @@ -2824,7 +2834,7 @@ { "from": "R", "to": "H", - "weight": 0.067672 + "weight": 0.071663 }, { "from": "R", @@ -2834,7 +2844,7 @@ { "from": "R", "to": "K", - "weight": 0.02995 + "weight": 0.02962 }, { "from": "R", @@ -2849,49 +2859,49 @@ { "from": "R", "to": "N", - "weight": 0.0422 + "weight": 0.048229 }, { "from": "R", "to": "P", - "weight": 0.08461 + "weight": 0.082891 }, { "from": "R", "to": "Q", - "weight": 0.037346 + "weight": 0.03615 }, { "from": "R", "to": "S", - "weight": 0.040282 + "weight": 0.051417 }, { "from": "R", "to": "T", - "weight": 0.054267 + "weight": 0.055505 }, { "from": "R", "to": "V", - "weight": 0.04235 + "weight": 0.041445 }, { "from": "R", "to": "W", - "weight": 0.092033 + "weight": 0.094643 }, { "from": "R", "to": "Y", - "weight": 0.0622 + "weight": 0.066408 } ], "93": [ { "from": "A", "to": "S", - "weight": 0.041389 + "weight": 0.03977 }, { "from": "A", @@ -2918,12 +2928,12 @@ { "from": "Y", "to": "E", - "weight": 0.055362 + "weight": 0.054835 }, { "from": "Y", "to": "F", - "weight": 0.062931 + "weight": 0.069494 }, { "from": "Y", @@ -2938,37 +2948,37 @@ { "from": "Y", "to": "I", - "weight": 0.072119 + "weight": 0.075147 }, { "from": "Y", "to": "K", - "weight": 0.063276 + "weight": 0.069563 }, { "from": "Y", "to": "M", - "weight": 0.06129 + "weight": 0.0612 }, { "from": "Y", "to": "N", - "weight": 0.049675 + "weight": 0.052808 }, { "from": "Y", "to": "Q", - "weight": 0.062343 + "weight": 0.06965 }, { "from": "Y", "to": "R", - "weight": 0.08088 + "weight": 0.097165 }, { "from": "Y", "to": "S", - "weight": 0.063881 + "weight": 0.057361 }, { "from": "Y", @@ -2978,12 +2988,12 @@ { "from": "Y", "to": "V", - "weight": 0.05196 + "weight": 0.061362 }, { "from": "Y", "to": "W", - "weight": 0.050743 + "weight": 0.05025 } ], "96": [ @@ -3010,7 +3020,7 @@ { "from": "N", "to": "S", - "weight": 0.02045 + "weight": 0.026871 }, { "from": "N", @@ -3027,19 +3037,19 @@ { "from": "D", "to": "E", - "weight": 0.032138 + "weight": 0.033287 }, { "from": "D", "to": "V", - "weight": 0.031783 + "weight": 0.047786 } ], "102": [ { "from": "V", "to": "I", - "weight": 0.04822 + "weight": 0.0517 } ], "103": [ @@ -3051,7 +3061,7 @@ { "from": "P", "to": "D", - "weight": 0.041067 + "weight": 0.03095 }, { "from": "P", @@ -3071,7 +3081,7 @@ { "from": "P", "to": "I", - "weight": 0.022527 + "weight": 0.033317 }, { "from": "P", @@ -3091,7 +3101,7 @@ { "from": "P", "to": "Q", - "weight": 0.04085 + "weight": 0.042286 }, { "from": "P", @@ -3101,51 +3111,51 @@ { "from": "P", "to": "S", - "weight": 0.052067 + "weight": 0.04225 }, { "from": "P", "to": "T", - "weight": 0.0212 + "weight": 0.021967 }, { "from": "P", "to": "V", - "weight": 0.0528 + "weight": 0.06805 }, { "from": "P", "to": "W", - "weight": 0.045833 + "weight": 0.041629 }, { "from": "P", "to": "Y", - "weight": 0.0403 + "weight": 0.037271 } ], "104": [ { "from": "D", "to": "H", - "weight": 0.045173 + "weight": 0.043269 }, { "from": "D", "to": "Q", - "weight": 0.048115 + "weight": 0.048621 }, { "from": "D", "to": "Y", - "weight": 0.091633 + "weight": 0.099513 } ], "105": [ { "from": "Y", "to": "H", - "weight": 0.055262 + "weight": 0.056367 }, { "from": "Y", @@ -3157,12 +3167,12 @@ { "from": "A", "to": "D", - "weight": 0.056175 + "weight": 0.07164 }, { "from": "A", "to": "E", - "weight": 0.03277 + "weight": 0.030927 }, { "from": "A", @@ -3177,12 +3187,12 @@ { "from": "A", "to": "L", - "weight": 0.03814 + "weight": 0.0344 }, { "from": "A", "to": "M", - "weight": 0.041044 + "weight": 0.038983 }, { "from": "A", @@ -3192,17 +3202,17 @@ { "from": "A", "to": "Q", - "weight": 0.039208 + "weight": 0.037286 }, { "from": "A", "to": "S", - "weight": 0.033958 + "weight": 0.0329 }, { "from": "A", "to": "T", - "weight": 0.02904 + "weight": 0.030717 }, { "from": "A", @@ -3212,7 +3222,7 @@ { "from": "A", "to": "W", - "weight": 0.046178 + "weight": 0.04225 } ], "107": [ @@ -3234,7 +3244,7 @@ { "from": "S", "to": "T", - "weight": 0.0842 + "weight": 0.07645 }, { "from": "S", @@ -3244,7 +3254,7 @@ { "from": "S", "to": "Y", - "weight": 0.0198 + "weight": 0.0287 } ], "109": [ @@ -3270,21 +3280,21 @@ { "from": "V", "to": "I", - "weight": 0.042031 + "weight": 0.03996 } ], "113": [ { "from": "A", "to": "S", - "weight": 0.071362 + "weight": 0.0674 } ], "114": [ { "from": "S", "to": "A", - "weight": 0.06015 + "weight": 0.060924 }, { "from": "S", @@ -3294,7 +3304,7 @@ { "from": "S", "to": "E", - "weight": 0.053822 + "weight": 0.054658 }, { "from": "S", @@ -3309,17 +3319,17 @@ { "from": "S", "to": "L", - "weight": 0.02477 + "weight": 0.0245 }, { "from": "S", "to": "M", - "weight": 0.0498 + "weight": 0.07605 }, { "from": "S", "to": "N", - "weight": 0.052257 + "weight": 0.061225 }, { "from": "S", @@ -3329,7 +3339,7 @@ { "from": "S", "to": "R", - "weight": 0.046655 + "weight": 0.048115 }, { "from": "S", @@ -3346,7 +3356,7 @@ { "from": "S", "to": "A", - "weight": 0.032323 + "weight": 0.047453 }, { "from": "S", @@ -3356,12 +3366,12 @@ { "from": "S", "to": "L", - "weight": 0.039044 + "weight": 0.04058 }, { "from": "S", "to": "M", - "weight": 0.050245 + "weight": 0.058195 }, { "from": "S", @@ -3378,7 +3388,7 @@ { "from": "T", "to": "S", - "weight": 0.045736 + "weight": 0.042777 } ], "121": [ @@ -3410,12 +3420,12 @@ { "from": "K", "to": "H", - "weight": 0.053889 + "weight": 0.05009 }, { "from": "K", "to": "I", - "weight": 0.029775 + "weight": 0.0251 }, { "from": "K", @@ -3440,7 +3450,7 @@ { "from": "K", "to": "R", - "weight": 0.0329 + "weight": 0.035675 }, { "from": "K", @@ -3450,7 +3460,7 @@ { "from": "K", "to": "T", - "weight": 0.02704 + "weight": 0.023483 }, { "from": "K", @@ -3487,7 +3497,7 @@ { "from": "N", "to": "F", - "weight": 0.1225 + "weight": 0.0968 }, { "from": "N", @@ -3574,7 +3584,7 @@ { "from": "S", "to": "K", - "weight": 0.353669 + "weight": 0.342665 }, { "from": "S", @@ -3589,12 +3599,12 @@ { "from": "S", "to": "P", - "weight": 0.0465 + "weight": 0.0463 }, { "from": "S", "to": "Q", - "weight": 0.066775 + "weight": 0.05842 }, { "from": "S", @@ -3628,7 +3638,7 @@ { "from": "A", "to": "D", - "weight": 0.029882 + "weight": 0.032174 }, { "from": "A", @@ -3638,7 +3648,7 @@ { "from": "A", "to": "F", - "weight": 0.040162 + "weight": 0.038876 }, { "from": "A", @@ -3653,7 +3663,7 @@ { "from": "A", "to": "I", - "weight": 0.04315 + "weight": 0.042 }, { "from": "A", @@ -3668,22 +3678,22 @@ { "from": "A", "to": "M", - "weight": 0.047533 + "weight": 0.043914 }, { "from": "A", "to": "N", - "weight": 0.043192 + "weight": 0.044736 }, { "from": "A", "to": "P", - "weight": 0.035213 + "weight": 0.03852 }, { "from": "A", "to": "Q", - "weight": 0.047736 + "weight": 0.047419 }, { "from": "A", @@ -3693,7 +3703,7 @@ { "from": "A", "to": "S", - "weight": 0.0518 + "weight": 0.04914 }, { "from": "A", @@ -3703,12 +3713,12 @@ { "from": "A", "to": "V", - "weight": 0.057356 + "weight": 0.058289 }, { "from": "A", "to": "W", - "weight": 0.0769 + "weight": 0.072833 }, { "from": "A", @@ -3725,12 +3735,12 @@ { "from": "T", "to": "E", - "weight": 0.102275 + "weight": 0.110665 }, { "from": "T", "to": "K", - "weight": 0.187589 + "weight": 0.18298 }, { "from": "T", @@ -3745,48 +3755,48 @@ { "from": "T", "to": "Q", - "weight": 0.099213 + "weight": 0.090694 }, { "from": "T", "to": "R", - "weight": 0.37268 + "weight": 0.313483 }, { "from": "T", "to": "S", - "weight": 0.029711 + "weight": 0.04461 }, { "from": "T", "to": "V", - "weight": 0.06875 + "weight": 0.068162 } ], "132": [ { "from": "Q", "to": "E", - "weight": 0.046406 + "weight": 0.05421 } ], "133": [ { "from": "N", "to": "D", - "weight": 0.081062 + "weight": 0.085667 }, { "from": "N", "to": "S", - "weight": 0.028967 + "weight": 0.04552 } ], "135": [ { "from": "K", "to": "A", - "weight": 0.084964 + "weight": 0.102275 }, { "from": "K", @@ -3796,17 +3806,17 @@ { "from": "K", "to": "D", - "weight": 0.096212 + "weight": 0.1186 }, { "from": "K", "to": "E", - "weight": 0.201838 + "weight": 0.231883 }, { "from": "K", "to": "F", - "weight": 0.077618 + "weight": 0.077277 }, { "from": "K", @@ -3816,12 +3826,12 @@ { "from": "K", "to": "H", - "weight": 0.144 + "weight": 0.139167 }, { "from": "K", "to": "I", - "weight": 0.1065 + "weight": 0.220543 }, { "from": "K", @@ -3836,7 +3846,7 @@ { "from": "K", "to": "N", - "weight": 0.077218 + "weight": 0.092822 }, { "from": "K", @@ -3851,7 +3861,7 @@ { "from": "K", "to": "S", - "weight": 0.134193 + "weight": 0.158925 }, { "from": "K", @@ -3861,12 +3871,12 @@ { "from": "K", "to": "V", - "weight": 0.110338 + "weight": 0.220736 }, { "from": "K", "to": "Y", - "weight": 0.0631 + "weight": 0.059567 } ], "136": [ @@ -3880,22 +3890,22 @@ { "from": "F", "to": "A", - "weight": 0.169974 + "weight": 0.271781 }, { "from": "F", "to": "G", - "weight": 0.134 + "weight": 0.163262 }, { "from": "F", "to": "S", - "weight": 0.177976 + "weight": 0.324711 }, { "from": "F", "to": "Y", - "weight": 0.035215 + "weight": 0.035971 } ], "138": [ @@ -3919,7 +3929,7 @@ { "from": "I", "to": "M", - "weight": 0.210464 + "weight": 0.210627 }, { "from": "I", @@ -3929,41 +3939,41 @@ { "from": "I", "to": "P", - "weight": 0.075427 + "weight": 0.071458 }, { "from": "I", "to": "Q", - "weight": 0.070067 + "weight": 0.06466 } ], "141": [ { "from": "R", "to": "S", - "weight": 0.060223 + "weight": 0.056964 } ], "142": [ { "from": "G", "to": "A", - "weight": 0.047488 + "weight": 0.057356 }, { "from": "G", "to": "D", - "weight": 0.057627 + "weight": 0.070524 }, { "from": "G", "to": "E", - "weight": 0.07059 + "weight": 0.062592 }, { "from": "G", "to": "H", - "weight": 0.0557 + "weight": 0.082247 }, { "from": "G", @@ -3973,12 +3983,12 @@ { "from": "G", "to": "N", - "weight": 0.093671 + "weight": 0.097846 }, { "from": "G", "to": "Q", - "weight": 0.0479 + "weight": 0.076643 }, { "from": "G", @@ -3988,39 +3998,39 @@ { "from": "G", "to": "S", - "weight": 0.055264 + "weight": 0.064942 }, { "from": "G", "to": "Y", - "weight": 0.042345 + "weight": 0.040362 } ], "143": [ { "from": "S", "to": "A", - "weight": 0.070179 + "weight": 0.068347 }, { "from": "S", "to": "D", - "weight": 0.103026 + "weight": 0.108829 }, { "from": "S", "to": "E", - "weight": 0.101929 + "weight": 0.106661 }, { "from": "S", "to": "G", - "weight": 0.09 + "weight": 0.098382 }, { "from": "S", "to": "H", - "weight": 0.08934 + "weight": 0.079183 }, { "from": "S", @@ -4030,22 +4040,22 @@ { "from": "S", "to": "M", - "weight": 0.03582 + "weight": 0.050157 }, { "from": "S", "to": "N", - "weight": 0.186744 + "weight": 0.214289 }, { "from": "S", "to": "Q", - "weight": 0.044713 + "weight": 0.060244 }, { "from": "S", "to": "T", - "weight": 0.058271 + "weight": 0.059444 }, { "from": "S", @@ -4055,7 +4065,7 @@ { "from": "S", "to": "Y", - "weight": 0.056733 + "weight": 0.0524 } ], "144": [ @@ -4067,17 +4077,17 @@ { "from": "S", "to": "D", - "weight": 0.147329 + "weight": 0.175573 }, { "from": "S", "to": "E", - "weight": 0.158013 + "weight": 0.18242 }, { "from": "S", "to": "F", - "weight": 0.098425 + "weight": 0.08305 }, { "from": "S", @@ -4087,12 +4097,12 @@ { "from": "S", "to": "H", - "weight": 0.050069 + "weight": 0.046764 }, { "from": "S", "to": "K", - "weight": 0.103567 + "weight": 0.130792 }, { "from": "S", @@ -4102,27 +4112,27 @@ { "from": "S", "to": "M", - "weight": 0.073067 + "weight": 0.10295 }, { "from": "S", "to": "N", - "weight": 0.313246 + "weight": 0.337365 }, { "from": "S", "to": "Q", - "weight": 0.084123 + "weight": 0.08525 }, { "from": "S", "to": "R", - "weight": 0.01755 + "weight": 0.02902 }, { "from": "S", "to": "T", - "weight": 0.04945 + "weight": 0.055153 }, { "from": "S", @@ -4144,17 +4154,17 @@ { "from": "S", "to": "E", - "weight": 0.256536 + "weight": 0.289513 }, { "from": "S", "to": "G", - "weight": 0.086745 + "weight": 0.083462 }, { "from": "S", "to": "H", - "weight": 0.114919 + "weight": 0.185494 }, { "from": "S", @@ -4164,41 +4174,41 @@ { "from": "S", "to": "K", - "weight": 0.499319 + "weight": 0.615161 }, { "from": "S", "to": "N", - "weight": 0.128009 + "weight": 0.2632 }, { "from": "S", "to": "P", - "weight": 0.1414 + "weight": 0.146271 }, { "from": "S", "to": "Q", - "weight": 0.194692 + "weight": 0.276604 }, { "from": "S", "to": "T", - "weight": 0.0319 + "weight": 0.228683 } ], "150": [ { "from": "R", "to": "K", - "weight": 0.028612 + "weight": 0.0304 } ], "155": [ { "from": "T", "to": "S", - "weight": 0.043817 + "weight": 0.0383 } ], "156": [ @@ -4289,7 +4299,7 @@ { "from": "N", "to": "D", - "weight": 0.1297 + "weight": 0.102275 } ], "159": [ @@ -4301,12 +4311,12 @@ { "from": "Y", "to": "D", - "weight": 0.303869 + "weight": 0.288688 }, { "from": "Y", "to": "E", - "weight": 0.279125 + "weight": 0.266835 }, { "from": "Y", @@ -4321,12 +4331,12 @@ { "from": "Y", "to": "H", - "weight": 0.143364 + "weight": 0.145217 }, { "from": "Y", "to": "K", - "weight": 0.235583 + "weight": 0.202443 }, { "from": "Y", @@ -4341,7 +4351,7 @@ { "from": "Y", "to": "N", - "weight": 0.262985 + "weight": 0.248929 }, { "from": "Y", @@ -4361,14 +4371,14 @@ { "from": "Y", "to": "W", - "weight": 0.19205 + "weight": 0.175525 } ], "160": [ { "from": "T", "to": "A", - "weight": 0.147675 + "weight": 0.16026 }, { "from": "T", @@ -4383,12 +4393,12 @@ { "from": "T", "to": "F", - "weight": 0.14255 + "weight": 0.1138 }, { "from": "T", "to": "H", - "weight": 0.23468 + "weight": 0.198617 }, { "from": "T", @@ -4398,37 +4408,37 @@ { "from": "T", "to": "K", - "weight": 0.255075 + "weight": 0.26338 }, { "from": "T", "to": "M", - "weight": 0.161333 + "weight": 0.147725 }, { "from": "T", "to": "N", - "weight": 0.1801 + "weight": 0.20406 }, { "from": "T", "to": "Q", - "weight": 0.2682 + "weight": 0.2279 }, { "from": "T", "to": "R", - "weight": 0.2894 + "weight": 0.251175 }, { "from": "T", "to": "S", - "weight": 0.010822 + "weight": 0.019109 }, { "from": "T", "to": "V", - "weight": 0.174025 + "weight": 0.1547 }, { "from": "T", @@ -4440,7 +4450,7 @@ { "from": "A", "to": "D", - "weight": 0.058414 + "weight": 0.0597 }, { "from": "A", @@ -4450,12 +4460,12 @@ { "from": "A", "to": "F", - "weight": 0.039433 + "weight": 0.03959 }, { "from": "A", "to": "H", - "weight": 0.076525 + "weight": 0.073757 }, { "from": "A", @@ -4480,7 +4490,7 @@ { "from": "A", "to": "P", - "weight": 0.069265 + "weight": 0.070811 }, { "from": "A", @@ -4517,19 +4527,19 @@ { "from": "L", "to": "Q", - "weight": 0.0607 + "weight": 0.063287 } ], "166": [ { "from": "V", "to": "A", - "weight": 0.106855 + "weight": 0.097569 }, { "from": "V", "to": "M", - "weight": 0.070162 + "weight": 0.067293 } ], "167": [ @@ -4541,12 +4551,12 @@ { "from": "T", "to": "I", - "weight": 0.0723 + "weight": 0.073413 }, { "from": "T", "to": "S", - "weight": 0.031122 + "weight": 0.03124 } ], "168": [ @@ -4558,7 +4568,7 @@ { "from": "M", "to": "Q", - "weight": 0.052614 + "weight": 0.054893 } ], "169": [ @@ -4577,7 +4587,7 @@ { "from": "K", "to": "A", - "weight": 0.0222 + "weight": 0.055614 }, { "from": "K", @@ -4587,7 +4597,7 @@ { "from": "K", "to": "D", - "weight": 0.06685 + "weight": 0.065353 }, { "from": "K", @@ -4597,27 +4607,27 @@ { "from": "K", "to": "F", - "weight": 0.032189 + "weight": 0.04649 }, { "from": "K", "to": "G", - "weight": 0.03771 + "weight": 0.042391 }, { "from": "K", "to": "H", - "weight": 0.04043 + "weight": 0.037255 }, { "from": "K", "to": "I", - "weight": 0.043054 + "weight": 0.04098 }, { "from": "K", "to": "L", - "weight": 0.042171 + "weight": 0.038613 }, { "from": "K", @@ -4637,17 +4647,17 @@ { "from": "K", "to": "R", - "weight": 0.034078 + "weight": 0.039318 }, { "from": "K", "to": "S", - "weight": 0.053962 + "weight": 0.051064 }, { "from": "K", "to": "T", - "weight": 0.032492 + "weight": 0.029387 }, { "from": "K", @@ -4662,14 +4672,14 @@ { "from": "K", "to": "Y", - "weight": 0.0313 + "weight": 0.038492 } ], "172": [ { "from": "E", "to": "D", - "weight": 0.043754 + "weight": 0.042093 }, { "from": "E", @@ -4686,12 +4696,12 @@ { "from": "Q", "to": "A", - "weight": 0.050656 + "weight": 0.04697 }, { "from": "Q", "to": "C", - "weight": 0.060175 + "weight": 0.057269 }, { "from": "Q", @@ -4701,7 +4711,7 @@ { "from": "Q", "to": "E", - "weight": 0.078336 + "weight": 0.076767 }, { "from": "Q", @@ -4716,7 +4726,7 @@ { "from": "Q", "to": "H", - "weight": 0.0326 + "weight": 0.030429 }, { "from": "Q", @@ -4736,32 +4746,32 @@ { "from": "Q", "to": "M", - "weight": 0.025833 + "weight": 0.02959 }, { "from": "Q", "to": "N", - "weight": 0.090008 + "weight": 0.084421 }, { "from": "Q", "to": "P", - "weight": 0.05047 + "weight": 0.047691 }, { "from": "Q", "to": "S", - "weight": 0.04965 + "weight": 0.044036 }, { "from": "Q", "to": "T", - "weight": 0.075163 + "weight": 0.073225 }, { "from": "Q", "to": "V", - "weight": 0.059929 + "weight": 0.060175 }, { "from": "Q", @@ -4771,7 +4781,7 @@ { "from": "Q", "to": "Y", - "weight": 0.053383 + "weight": 0.061536 } ], "174": [ @@ -4783,7 +4793,7 @@ { "from": "F", "to": "Y", - "weight": 0.045131 + "weight": 0.047736 } ], "175": [ @@ -4795,7 +4805,7 @@ { "from": "D", "to": "T", - "weight": 0.06545 + "weight": 0.0671 } ], "179": [ @@ -4809,7 +4819,7 @@ { "from": "V", "to": "I", - "weight": 0.071407 + "weight": 0.067587 } ], "184": [ @@ -4828,42 +4838,57 @@ { "from": "G", "to": "A", - "weight": 0.050713 + "weight": 0.098267 }, { "from": "G", "to": "C", - "weight": 0.0122 + "weight": 0.0877 }, { "from": "G", "to": "D", - "weight": 0.125533 + "weight": 0.139657 }, { "from": "G", "to": "E", - "weight": 0.145832 + "weight": 0.149867 }, { "from": "G", "to": "F", - "weight": 0.046933 + "weight": 0.03506 }, { "from": "G", "to": "H", - "weight": 0.074369 + "weight": 0.080722 }, { "from": "G", "to": "I", - "weight": 0.0361 + "weight": 0.0381 + }, + { + "from": "G", + "to": "L", + "weight": 0.0799 + }, + { + "from": "G", + "to": "M", + "weight": 0.0674 + }, + { + "from": "G", + "to": "N", + "weight": 0.3024 }, { "from": "G", "to": "P", - "weight": 0.109175 + "weight": 0.123041 }, { "from": "G", @@ -4873,7 +4898,12 @@ { "from": "G", "to": "S", - "weight": 0.055217 + "weight": 0.140414 + }, + { + "from": "G", + "to": "T", + "weight": 0.0124 }, { "from": "G", @@ -4883,7 +4913,7 @@ { "from": "G", "to": "W", - "weight": 0.085067 + "weight": 0.085238 }, { "from": "G", @@ -4895,12 +4925,12 @@ { "from": "T", "to": "A", - "weight": 0.060788 + "weight": 0.058856 }, { "from": "T", "to": "D", - "weight": 0.206282 + "weight": 0.21015 }, { "from": "T", @@ -4910,12 +4940,12 @@ { "from": "T", "to": "N", - "weight": 0.064787 + "weight": 0.062641 }, { "from": "T", "to": "S", - "weight": 0.115548 + "weight": 0.12533 } ], "188": [ @@ -4927,7 +4957,7 @@ { "from": "D", "to": "E", - "weight": 0.04561 + "weight": 0.048773 }, { "from": "D", @@ -4937,7 +4967,7 @@ { "from": "D", "to": "I", - "weight": 0.03225 + "weight": 0.025067 }, { "from": "D", @@ -4974,57 +5004,57 @@ { "from": "K", "to": "A", - "weight": 0.501592 + "weight": 0.497915 }, { "from": "K", "to": "D", - "weight": 0.60407 + "weight": 0.600672 }, { "from": "K", "to": "E", - "weight": 0.648465 + "weight": 0.654929 }, { "from": "K", "to": "F", - "weight": 0.313579 + "weight": 0.299495 }, { "from": "K", "to": "G", - "weight": 0.399288 + "weight": 0.381385 }, { "from": "K", "to": "H", - "weight": 0.348781 + "weight": 0.337868 }, { "from": "K", "to": "I", - "weight": 0.422933 + "weight": 0.419373 }, { "from": "K", "to": "L", - "weight": 0.426743 + "weight": 0.420396 }, { "from": "K", "to": "M", - "weight": 0.490091 + "weight": 0.486161 }, { "from": "K", "to": "N", - "weight": 0.447278 + "weight": 0.432792 }, { "from": "K", "to": "Q", - "weight": 0.52707 + "weight": 0.521787 }, { "from": "K", @@ -5034,22 +5064,22 @@ { "from": "K", "to": "S", - "weight": 0.463228 + "weight": 0.454719 }, { "from": "K", "to": "T", - "weight": 0.467905 + "weight": 0.461786 }, { "from": "K", "to": "V", - "weight": 0.45645 + "weight": 0.448148 }, { "from": "K", "to": "Y", - "weight": 0.30119 + "weight": 0.290864 } ], "190": [ @@ -5078,27 +5108,27 @@ { "from": "I", "to": "D", - "weight": 0.11714 + "weight": 0.1076 }, { "from": "I", "to": "E", - "weight": 0.163219 + "weight": 0.159013 }, { "from": "I", "to": "F", - "weight": 0.075581 + "weight": 0.072141 }, { "from": "I", "to": "H", - "weight": 0.060673 + "weight": 0.058987 }, { "from": "I", "to": "K", - "weight": 0.054811 + "weight": 0.05316 }, { "from": "I", @@ -5118,7 +5148,7 @@ { "from": "I", "to": "Q", - "weight": 0.0642 + "weight": 0.067936 }, { "from": "I", @@ -5143,29 +5173,29 @@ { "from": "I", "to": "W", - "weight": 0.110793 + "weight": 0.104044 }, { "from": "I", "to": "Y", - "weight": 0.075 + "weight": 0.086453 } ], "193": [ { "from": "S", "to": "A", - "weight": 0.11505 + "weight": 0.109591 }, { "from": "S", "to": "D", - "weight": 0.531852 + "weight": 0.562415 }, { "from": "S", "to": "E", - "weight": 0.517175 + "weight": 0.5026 }, { "from": "S", @@ -5207,7 +5237,7 @@ { "from": "A", "to": "G", - "weight": 0.079794 + "weight": 0.077895 }, { "from": "A", @@ -5217,12 +5247,12 @@ { "from": "A", "to": "S", - "weight": 0.052571 + "weight": 0.052244 }, { "from": "A", "to": "T", - "weight": 0.09712 + "weight": 0.082583 }, { "from": "A", @@ -5234,12 +5264,12 @@ { "from": "Q", "to": "A", - "weight": 0.034243 + "weight": 0.030113 }, { "from": "Q", "to": "C", - "weight": 0.075383 + "weight": 0.075492 }, { "from": "Q", @@ -5254,37 +5284,37 @@ { "from": "Q", "to": "G", - "weight": 0.0243 + "weight": 0.021575 }, { "from": "Q", "to": "H", - "weight": 0.059376 + "weight": 0.05803 }, { "from": "Q", "to": "I", - "weight": 0.060988 + "weight": 0.058356 }, { "from": "Q", "to": "K", - "weight": 0.04263 + "weight": 0.0504 }, { "from": "Q", "to": "M", - "weight": 0.050467 + "weight": 0.04552 }, { "from": "Q", "to": "N", - "weight": 0.11155 + "weight": 0.110262 }, { "from": "Q", "to": "R", - "weight": 0.05026 + "weight": 0.055112 }, { "from": "Q", @@ -5294,19 +5324,19 @@ { "from": "Q", "to": "T", - "weight": 0.043087 + "weight": 0.041506 }, { "from": "Q", "to": "V", - "weight": 0.048407 + "weight": 0.054193 } ], "198": [ { "from": "S", "to": "A", - "weight": 0.075956 + "weight": 0.080063 }, { "from": "S", @@ -5316,67 +5346,67 @@ { "from": "S", "to": "E", - "weight": 0.038183 + "weight": 0.051423 }, { "from": "S", "to": "F", - "weight": 0.017112 + "weight": 0.027956 }, { "from": "S", "to": "G", - "weight": 0.036573 + "weight": 0.037842 }, { "from": "S", "to": "H", - "weight": 0.03314 + "weight": 0.03325 }, { "from": "S", "to": "I", - "weight": 0.059243 + "weight": 0.054363 }, { "from": "S", "to": "K", - "weight": 0.053773 + "weight": 0.052581 }, { "from": "S", "to": "L", - "weight": 0.04296 + "weight": 0.041327 }, { "from": "S", "to": "M", - "weight": 0.046767 + "weight": 0.048926 }, { "from": "S", "to": "N", - "weight": 0.019333 + "weight": 0.029391 }, { "from": "S", "to": "P", - "weight": 0.041026 + "weight": 0.045745 }, { "from": "S", "to": "Q", - "weight": 0.040679 + "weight": 0.038307 }, { "from": "S", "to": "R", - "weight": 0.071817 + "weight": 0.067986 }, { "from": "S", "to": "T", - "weight": 0.02935 + "weight": 0.027878 }, { "from": "S", @@ -5393,7 +5423,7 @@ { "from": "S", "to": "A", - "weight": 0.030267 + "weight": 0.050227 }, { "from": "S", @@ -5403,42 +5433,42 @@ { "from": "S", "to": "E", - "weight": 0.043585 + "weight": 0.04551 }, { "from": "S", "to": "G", - "weight": 0.091833 + "weight": 0.088881 }, { "from": "S", "to": "H", - "weight": 0.051894 + "weight": 0.053978 }, { "from": "S", "to": "I", - "weight": 0.0372 + "weight": 0.03643 }, { "from": "S", "to": "K", - "weight": 0.052756 + "weight": 0.053027 }, { "from": "S", "to": "L", - "weight": 0.046617 + "weight": 0.053885 }, { "from": "S", "to": "M", - "weight": 0.034391 + "weight": 0.035923 }, { "from": "S", "to": "N", - "weight": 0.054769 + "weight": 0.072807 }, { "from": "S", @@ -5448,12 +5478,12 @@ { "from": "S", "to": "Q", - "weight": 0.038233 + "weight": 0.040569 }, { "from": "S", "to": "T", - "weight": 0.0485 + "weight": 0.046124 }, { "from": "S", @@ -5468,7 +5498,7 @@ { "from": "S", "to": "Y", - "weight": 0.042107 + "weight": 0.046 } ], "200": [ @@ -5485,7 +5515,7 @@ { "from": "G", "to": "P", - "weight": 0.074737 + "weight": 0.0704 }, { "from": "G", @@ -5502,7 +5532,7 @@ { "from": "R", "to": "A", - "weight": 0.0567 + "weight": 0.053273 }, { "from": "R", @@ -5512,27 +5542,27 @@ { "from": "R", "to": "E", - "weight": 0.053375 + "weight": 0.071767 }, { "from": "R", "to": "F", - "weight": 0.052811 + "weight": 0.05064 }, { "from": "R", "to": "G", - "weight": 0.052723 + "weight": 0.051493 }, { "from": "R", "to": "H", - "weight": 0.044731 + "weight": 0.044507 }, { "from": "R", "to": "I", - "weight": 0.052847 + "weight": 0.0538 }, { "from": "R", @@ -5557,22 +5587,22 @@ { "from": "R", "to": "P", - "weight": 0.078929 + "weight": 0.075733 }, { "from": "R", "to": "Q", - "weight": 0.042527 + "weight": 0.043181 }, { "from": "R", "to": "S", - "weight": 0.069971 + "weight": 0.068593 }, { "from": "R", "to": "T", - "weight": 0.038781 + "weight": 0.040388 }, { "from": "R", @@ -5594,7 +5624,7 @@ { "from": "I", "to": "V", - "weight": 0.047573 + "weight": 0.044894 } ], "203": [ @@ -5606,7 +5636,7 @@ { "from": "T", "to": "E", - "weight": 0.05715 + "weight": 0.0762 }, { "from": "T", @@ -5616,7 +5646,7 @@ { "from": "T", "to": "M", - "weight": 0.031325 + "weight": 0.0291 }, { "from": "T", @@ -5633,39 +5663,39 @@ { "from": "S", "to": "Y", - "weight": 0.034933 + "weight": 0.02835 } ], "207": [ { "from": "K", "to": "A", - "weight": 0.046633 + "weight": 0.044419 }, { "from": "K", "to": "G", - "weight": 0.045467 + "weight": 0.044223 }, { "from": "K", "to": "M", - "weight": 0.04089 + "weight": 0.042009 }, { "from": "K", "to": "Q", - "weight": 0.05735 + "weight": 0.058695 }, { "from": "K", "to": "R", - "weight": 0.066778 + "weight": 0.071368 }, { "from": "K", "to": "S", - "weight": 0.043719 + "weight": 0.041506 }, { "from": "K", @@ -5677,7 +5707,7 @@ { "from": "R", "to": "A", - "weight": 0.025864 + "weight": 0.024283 }, { "from": "R", @@ -5692,7 +5722,7 @@ { "from": "R", "to": "F", - "weight": 0.05364 + "weight": 0.053881 }, { "from": "R", @@ -5707,17 +5737,17 @@ { "from": "R", "to": "I", - "weight": 0.042181 + "weight": 0.046088 }, { "from": "R", "to": "K", - "weight": 0.05045 + "weight": 0.044629 }, { "from": "R", "to": "L", - "weight": 0.057829 + "weight": 0.059419 }, { "from": "R", @@ -5732,7 +5762,7 @@ { "from": "R", "to": "Q", - "weight": 0.049138 + "weight": 0.054765 }, { "from": "R", @@ -5747,7 +5777,7 @@ { "from": "R", "to": "V", - "weight": 0.047536 + "weight": 0.051194 }, { "from": "R", @@ -5759,7 +5789,7 @@ { "from": "S", "to": "I", - "weight": 0.032663 + "weight": 0.031622 }, { "from": "S", @@ -5769,7 +5799,7 @@ { "from": "S", "to": "T", - "weight": 0.032083 + "weight": 0.039292 } ], "210": [ @@ -5781,7 +5811,7 @@ { "from": "Q", "to": "I", - "weight": 0.048533 + "weight": 0.044 }, { "from": "Q", @@ -5798,7 +5828,7 @@ { "from": "A", "to": "D", - "weight": 0.0609 + "weight": 0.06975 }, { "from": "A", @@ -5823,14 +5853,14 @@ { "from": "A", "to": "V", - "weight": 0.080511 + "weight": 0.088895 } ], "213": [ { "from": "V", "to": "A", - "weight": 0.087337 + "weight": 0.081222 }, { "from": "V", @@ -5847,17 +5877,17 @@ { "from": "I", "to": "E", - "weight": 0.050037 + "weight": 0.04835 }, { "from": "I", "to": "F", - "weight": 0.0452 + "weight": 0.04492 }, { "from": "I", "to": "G", - "weight": 0.074677 + "weight": 0.078321 }, { "from": "I", @@ -5867,27 +5897,27 @@ { "from": "I", "to": "K", - "weight": 0.073283 + "weight": 0.082954 }, { "from": "I", "to": "L", - "weight": 0.041217 + "weight": 0.082671 }, { "from": "I", "to": "M", - "weight": 0.039073 + "weight": 0.049431 }, { "from": "I", "to": "Q", - "weight": 0.053618 + "weight": 0.051411 }, { "from": "I", "to": "R", - "weight": 0.081047 + "weight": 0.07708 }, { "from": "I", @@ -5897,7 +5927,7 @@ { "from": "I", "to": "T", - "weight": 0.032121 + "weight": 0.03078 }, { "from": "I", @@ -5907,12 +5937,12 @@ { "from": "I", "to": "W", - "weight": 0.051182 + "weight": 0.04755 }, { "from": "I", "to": "Y", - "weight": 0.052638 + "weight": 0.052287 } ], "215": [ @@ -5941,12 +5971,12 @@ { "from": "N", "to": "A", - "weight": 0.051718 + "weight": 0.048008 }, { "from": "N", "to": "D", - "weight": 0.025989 + "weight": 0.03168 }, { "from": "N", @@ -5956,22 +5986,22 @@ { "from": "N", "to": "F", - "weight": 0.047008 + "weight": 0.048308 }, { "from": "N", "to": "H", - "weight": 0.063889 + "weight": 0.062362 }, { "from": "N", "to": "I", - "weight": 0.025111 + "weight": 0.03756 }, { "from": "N", "to": "K", - "weight": 0.051385 + "weight": 0.057973 }, { "from": "N", @@ -5981,22 +6011,22 @@ { "from": "N", "to": "M", - "weight": 0.07828 + "weight": 0.075927 }, { "from": "N", "to": "Q", - "weight": 0.074588 + "weight": 0.069853 }, { "from": "N", "to": "R", - "weight": 0.058924 + "weight": 0.071878 }, { "from": "N", "to": "S", - "weight": 0.053536 + "weight": 0.052207 }, { "from": "N", @@ -6011,14 +6041,14 @@ { "from": "N", "to": "Y", - "weight": 0.041018 + "weight": 0.04115 } ], "217": [ { "from": "I", "to": "L", - "weight": 0.00855 + "weight": 0.082833 }, { "from": "I", @@ -6030,7 +6060,7 @@ { "from": "G", "to": "A", - "weight": 0.0411 + "weight": 0.045533 }, { "from": "G", @@ -6050,7 +6080,7 @@ { "from": "G", "to": "I", - "weight": 0.112135 + "weight": 0.108022 }, { "from": "G", @@ -6097,7 +6127,7 @@ { "from": "S", "to": "E", - "weight": 0.071768 + "weight": 0.080695 }, { "from": "S", @@ -6107,7 +6137,7 @@ { "from": "S", "to": "G", - "weight": 0.029544 + "weight": 0.02937 }, { "from": "S", @@ -6117,7 +6147,7 @@ { "from": "S", "to": "I", - "weight": 0.05105 + "weight": 0.056038 }, { "from": "S", @@ -6127,7 +6157,7 @@ { "from": "S", "to": "L", - "weight": 0.075187 + "weight": 0.071144 }, { "from": "S", @@ -6137,34 +6167,39 @@ { "from": "S", "to": "N", - "weight": 0.0436 + "weight": 0.04938 }, { "from": "S", "to": "Q", - "weight": 0.02446 + "weight": 0.02335 }, { "from": "S", "to": "T", - "weight": 0.05923 + "weight": 0.058045 }, { "from": "S", "to": "V", - "weight": 0.058308 + "weight": 0.06572 } ], "220": [ { "from": "R", "to": "A", - "weight": 0.0157 + "weight": 0.0887 + }, + { + "from": "R", + "to": "C", + "weight": 0.0201 }, { "from": "R", "to": "F", - "weight": 0.02345 + "weight": 0.037533 }, { "from": "R", @@ -6194,7 +6229,12 @@ { "from": "R", "to": "S", - "weight": 0.0052 + "weight": 0.073767 + }, + { + "from": "R", + "to": "V", + "weight": 0.1893 }, { "from": "R", @@ -6204,14 +6244,14 @@ { "from": "R", "to": "Y", - "weight": 0.02435 + "weight": 0.038033 } ], "221": [ { "from": "P", "to": "A", - "weight": 0.084768 + "weight": 0.084505 }, { "from": "P", @@ -6221,7 +6261,7 @@ { "from": "P", "to": "T", - "weight": 0.117656 + "weight": 0.108928 } ], "222": [ @@ -6243,12 +6283,12 @@ { "from": "R", "to": "H", - "weight": 0.079186 + "weight": 0.081775 }, { "from": "R", "to": "I", - "weight": 0.044675 + "weight": 0.05794 }, { "from": "R", @@ -6263,7 +6303,7 @@ { "from": "R", "to": "M", - "weight": 0.053622 + "weight": 0.04856 }, { "from": "R", @@ -6298,12 +6338,12 @@ { "from": "R", "to": "W", - "weight": 0.025967 + "weight": 0.030675 }, { "from": "R", "to": "Y", - "weight": 0.093233 + "weight": 0.0728 } ], "223": [ @@ -6356,10 +6396,20 @@ } ], "225": [ + { + "from": "D", + "to": "E", + "weight": 0.1315 + }, + { + "from": "D", + "to": "N", + "weight": 0.1098 + }, { "from": "D", "to": "T", - "weight": 0.0292 + "weight": 0.48785 } ], "226": [ @@ -6371,17 +6421,17 @@ { "from": "I", "to": "M", - "weight": 0.06172 + "weight": 0.1067 }, { "from": "I", "to": "Q", - "weight": 0.1155 + "weight": 0.2897 }, { "from": "I", "to": "V", - "weight": 0.0907 + "weight": 0.070233 } ], "227": [ @@ -6408,7 +6458,7 @@ { "from": "P", "to": "H", - "weight": 0.033157 + "weight": 0.0362 }, { "from": "P", @@ -6450,31 +6500,31 @@ { "from": "S", "to": "A", - "weight": 0.042317 + "weight": 0.156586 } ], "229": [ { "from": "R", "to": "F", - "weight": 0.1 + "weight": 0.0737 }, { "from": "R", "to": "G", - "weight": 0.0287 + "weight": 0.2415 }, { "from": "R", "to": "I", - "weight": 0.0515 + "weight": 0.0565 } ], "230": [ { "from": "I", "to": "V", - "weight": 0.065787 + "weight": 0.0562 } ], "231": [ @@ -6486,12 +6536,12 @@ { "from": "S", "to": "Q", - "weight": 0.045943 + "weight": 0.052312 }, { "from": "S", "to": "T", - "weight": 0.023667 + "weight": 0.024 } ], "233": [ @@ -6534,7 +6584,7 @@ { "from": "K", "to": "P", - "weight": 0.050882 + "weight": 0.0484 }, { "from": "K", @@ -6544,7 +6594,7 @@ { "from": "K", "to": "R", - "weight": 0.026925 + "weight": 0.03042 } ], "242": [ @@ -6556,7 +6606,7 @@ { "from": "I", "to": "C", - "weight": 0.077294 + "weight": 0.077811 }, { "from": "I", @@ -6571,7 +6621,7 @@ { "from": "I", "to": "M", - "weight": 0.066395 + "weight": 0.074864 }, { "from": "I", @@ -6586,19 +6636,19 @@ { "from": "I", "to": "T", - "weight": 0.043317 + "weight": 0.038614 }, { "from": "I", "to": "V", - "weight": 0.048706 + "weight": 0.046717 } ], "244": [ { "from": "L", "to": "A", - "weight": 0.037914 + "weight": 0.037988 }, { "from": "L", @@ -6608,12 +6658,12 @@ { "from": "L", "to": "E", - "weight": 0.0296 + "weight": 0.038025 }, { "from": "L", "to": "F", - "weight": 0.102161 + "weight": 0.107889 }, { "from": "L", @@ -6623,12 +6673,12 @@ { "from": "L", "to": "I", - "weight": 0.12006 + "weight": 0.134656 }, { "from": "L", "to": "M", - "weight": 0.125006 + "weight": 0.144383 }, { "from": "L", @@ -6648,7 +6698,7 @@ { "from": "L", "to": "Y", - "weight": 0.152247 + "weight": 0.160733 } ], "246": [ @@ -6662,7 +6712,7 @@ { "from": "S", "to": "A", - "weight": 0.08554 + "weight": 0.083819 }, { "from": "S", @@ -6672,21 +6722,21 @@ { "from": "S", "to": "T", - "weight": 0.062873 + "weight": 0.075677 } ], "251": [ { "from": "L", "to": "F", - "weight": 0.036475 + "weight": 0.034854 } ], "258": [ { "from": "F", "to": "Y", - "weight": 0.042369 + "weight": 0.039628 } ], "259": [ @@ -6698,19 +6748,19 @@ { "from": "K", "to": "R", - "weight": 0.02795 + "weight": 0.0273 }, { "from": "K", "to": "V", - "weight": 0.069607 + "weight": 0.065033 } ], "260": [ { "from": "I", "to": "L", - "weight": 0.045584 + "weight": 0.04391 }, { "from": "I", @@ -6732,7 +6782,7 @@ { "from": "R", "to": "C", - "weight": 0.034525 + "weight": 0.08914 }, { "from": "R", @@ -6747,32 +6797,32 @@ { "from": "R", "to": "F", - "weight": 0.043158 + "weight": 0.040821 }, { "from": "R", "to": "G", - "weight": 0.03591 + "weight": 0.046381 }, { "from": "R", "to": "H", - "weight": 0.042322 + "weight": 0.047318 }, { "from": "R", "to": "I", - "weight": 0.0117 + "weight": 0.026317 }, { "from": "R", "to": "K", - "weight": 0.046353 + "weight": 0.044561 }, { "from": "R", "to": "L", - "weight": 0.036285 + "weight": 0.03432 }, { "from": "R", @@ -6782,22 +6832,22 @@ { "from": "R", "to": "N", - "weight": 0.031689 + "weight": 0.027618 }, { "from": "R", "to": "P", - "weight": 0.021557 + "weight": 0.028987 }, { "from": "R", "to": "Q", - "weight": 0.02584 + "weight": 0.028855 }, { "from": "R", "to": "S", - "weight": 0.027008 + "weight": 0.027979 }, { "from": "R", @@ -6807,7 +6857,7 @@ { "from": "R", "to": "V", - "weight": 0.0314 + "weight": 0.029978 }, { "from": "R", @@ -6824,27 +6874,27 @@ { "from": "S", "to": "A", - "weight": 0.03405 + "weight": 0.035118 }, { "from": "S", "to": "D", - "weight": 0.03296 + "weight": 0.067083 }, { "from": "S", "to": "E", - "weight": 0.047343 + "weight": 0.0483 }, { "from": "S", "to": "G", - "weight": 0.0441 + "weight": 0.04572 }, { "from": "S", "to": "H", - "weight": 0.035471 + "weight": 0.032025 }, { "from": "S", @@ -6859,7 +6909,7 @@ { "from": "S", "to": "M", - "weight": 0.0291 + "weight": 0.031792 }, { "from": "S", @@ -6869,17 +6919,17 @@ { "from": "S", "to": "P", - "weight": 0.04365 + "weight": 0.04168 }, { "from": "S", "to": "Q", - "weight": 0.036286 + "weight": 0.0382 }, { "from": "S", "to": "R", - "weight": 0.064206 + "weight": 0.062433 }, { "from": "S", @@ -6889,7 +6939,7 @@ { "from": "S", "to": "Y", - "weight": 0.02719 + "weight": 0.035055 } ], "263": [ @@ -6906,19 +6956,19 @@ { "from": "G", "to": "W", - "weight": 0.09499 + "weight": 0.091673 } ], "264": [ { "from": "K", "to": "A", - "weight": 0.023525 + "weight": 0.0242 }, { "from": "K", "to": "D", - "weight": 0.039345 + "weight": 0.040567 }, { "from": "K", @@ -6928,17 +6978,17 @@ { "from": "K", "to": "G", - "weight": 0.0382 + "weight": 0.06566 }, { "from": "K", "to": "H", - "weight": 0.0502 + "weight": 0.047915 }, { "from": "K", "to": "N", - "weight": 0.046411 + "weight": 0.047705 }, { "from": "K", @@ -6948,7 +6998,7 @@ { "from": "K", "to": "R", - "weight": 0.028562 + "weight": 0.0236 }, { "from": "K", @@ -6958,7 +7008,7 @@ { "from": "K", "to": "T", - "weight": 0.07 + "weight": 0.0484 } ], "265": [ @@ -6982,26 +7032,26 @@ { "from": "S", "to": "T", - "weight": 0.030687 + "weight": 0.043889 } ], "267": [ { "from": "I", "to": "V", - "weight": 0.045044 + "weight": 0.04581 } ], "268": [ { "from": "M", "to": "I", - "weight": 0.02328 + "weight": 0.025083 }, { "from": "M", "to": "L", - "weight": 0.025317 + "weight": 0.023487 } ], "269": [ @@ -7023,17 +7073,17 @@ { "from": "R", "to": "L", - "weight": 0.029167 + "weight": 0.025725 }, { "from": "R", "to": "M", - "weight": 0.032989 + "weight": 0.04537 }, { "from": "R", "to": "Q", - "weight": 0.05587 + "weight": 0.051692 }, { "from": "R", @@ -7043,65 +7093,65 @@ { "from": "R", "to": "V", - "weight": 0.0319 + "weight": 0.039086 } ], "270": [ { "from": "S", "to": "T", - "weight": 0.03045 + "weight": 0.028931 } ], "272": [ { "from": "A", "to": "L", - "weight": 0.041438 + "weight": 0.05525 }, { "from": "A", "to": "M", - "weight": 0.052318 + "weight": 0.04895 }, { "from": "A", "to": "T", - "weight": 0.049633 + "weight": 0.044 }, { "from": "A", "to": "V", - "weight": 0.031414 + "weight": 0.030287 } ], "273": [ { "from": "P", "to": "K", - "weight": 0.077567 + "weight": 0.0819 } ], "275": [ { "from": "G", "to": "A", - "weight": 0.067729 + "weight": 0.07382 }, { "from": "G", "to": "H", - "weight": 0.078882 + "weight": 0.08375 }, { "from": "G", "to": "I", - "weight": 0.127988 + "weight": 0.117533 }, { "from": "G", "to": "K", - "weight": 0.106628 + "weight": 0.1077 }, { "from": "G", @@ -7111,7 +7161,7 @@ { "from": "G", "to": "Q", - "weight": 0.079213 + "weight": 0.075872 }, { "from": "G", @@ -7126,7 +7176,7 @@ { "from": "G", "to": "T", - "weight": 0.067433 + "weight": 0.070558 }, { "from": "G", @@ -7148,12 +7198,12 @@ { "from": "K", "to": "I", - "weight": 0.0738 + "weight": 0.072375 }, { "from": "K", "to": "L", - "weight": 0.0571 + "weight": 0.061258 }, { "from": "K", @@ -7163,7 +7213,7 @@ { "from": "K", "to": "N", - "weight": 0.115847 + "weight": 0.11145 }, { "from": "K", @@ -7173,12 +7223,12 @@ { "from": "K", "to": "R", - "weight": 0.088309 + "weight": 0.0872 }, { "from": "K", "to": "S", - "weight": 0.095494 + "weight": 0.0893 }, { "from": "K", @@ -7190,7 +7240,7 @@ { "from": "K", "to": "A", - "weight": 0.046136 + "weight": 0.048133 }, { "from": "K", @@ -7200,7 +7250,7 @@ { "from": "K", "to": "E", - "weight": 0.030664 + "weight": 0.031858 }, { "from": "K", @@ -7210,32 +7260,32 @@ { "from": "K", "to": "H", - "weight": 0.046818 + "weight": 0.043742 }, { "from": "K", "to": "I", - "weight": 0.056476 + "weight": 0.064811 }, { "from": "K", "to": "L", - "weight": 0.054867 + "weight": 0.04997 }, { "from": "K", "to": "M", - "weight": 0.042033 + "weight": 0.039469 }, { "from": "K", "to": "N", - "weight": 0.031621 + "weight": 0.038125 }, { "from": "K", "to": "Q", - "weight": 0.0376 + "weight": 0.038327 }, { "from": "K", @@ -7250,44 +7300,44 @@ { "from": "K", "to": "T", - "weight": 0.04526 + "weight": 0.048091 }, { "from": "K", "to": "V", - "weight": 0.040947 + "weight": 0.038531 }, { "from": "K", "to": "W", - "weight": 0.030027 + "weight": 0.0381 }, { "from": "K", "to": "Y", - "weight": 0.035082 + "weight": 0.033358 } ], "279": [ { "from": "S", "to": "A", - "weight": 0.077727 + "weight": 0.076325 }, { "from": "S", "to": "C", - "weight": 0.051967 + "weight": 0.052192 }, { "from": "S", "to": "E", - "weight": 0.069837 + "weight": 0.065922 }, { "from": "S", "to": "F", - "weight": 0.031363 + "weight": 0.03819 }, { "from": "S", @@ -7297,7 +7347,7 @@ { "from": "S", "to": "H", - "weight": 0.051222 + "weight": 0.06376 }, { "from": "S", @@ -7312,27 +7362,27 @@ { "from": "S", "to": "L", - "weight": 0.040267 + "weight": 0.044029 }, { "from": "S", "to": "M", - "weight": 0.044427 + "weight": 0.043758 }, { "from": "S", "to": "N", - "weight": 0.040473 + "weight": 0.037617 }, { "from": "S", "to": "Q", - "weight": 0.048576 + "weight": 0.046356 }, { "from": "S", "to": "R", - "weight": 0.074825 + "weight": 0.08077 }, { "from": "S", @@ -7342,19 +7392,19 @@ { "from": "S", "to": "Y", - "weight": 0.045286 + "weight": 0.048087 } ], "280": [ { "from": "E", "to": "A", - "weight": 0.060959 + "weight": 0.063472 }, { "from": "E", "to": "D", - "weight": 0.0421 + "weight": 0.039133 }, { "from": "E", @@ -7364,12 +7414,12 @@ { "from": "E", "to": "G", - "weight": 0.085671 + "weight": 0.086762 }, { "from": "E", "to": "H", - "weight": 0.058767 + "weight": 0.053286 }, { "from": "E", @@ -7379,22 +7429,22 @@ { "from": "E", "to": "L", - "weight": 0.068146 + "weight": 0.063979 }, { "from": "E", "to": "M", - "weight": 0.034817 + "weight": 0.032308 }, { "from": "E", "to": "P", - "weight": 0.041592 + "weight": 0.04225 }, { "from": "E", "to": "Q", - "weight": 0.041978 + "weight": 0.0443 }, { "from": "E", @@ -7409,12 +7459,12 @@ { "from": "E", "to": "V", - "weight": 0.054244 + "weight": 0.05183 }, { "from": "E", "to": "W", - "weight": 0.035267 + "weight": 0.048136 } ], "282": [ @@ -7433,38 +7483,38 @@ { "from": "T", "to": "S", - "weight": 0.070587 + "weight": 0.06694 } ], "284": [ { "from": "P", "to": "A", - "weight": 0.0648 + "weight": 0.04815 } ], "288": [ { "from": "I", "to": "L", - "weight": 0.039689 + "weight": 0.03724 }, { "from": "I", "to": "M", - "weight": 0.0167 + "weight": 0.027862 } ], "289": [ { "from": "P", "to": "A", - "weight": 0.016113 + "weight": 0.015756 }, { "from": "P", "to": "E", - "weight": 0.05666 + "weight": 0.062483 }, { "from": "P", @@ -7479,24 +7529,24 @@ { "from": "P", "to": "T", - "weight": 0.031617 + "weight": 0.033614 } ], "290": [ { "from": "N", "to": "A", - "weight": 0.034408 + "weight": 0.040093 }, { "from": "N", "to": "G", - "weight": 0.077267 + "weight": 0.0948 }, { "from": "N", "to": "T", - "weight": 0.044456 + "weight": 0.05161 }, { "from": "N", @@ -7508,17 +7558,17 @@ { "from": "D", "to": "A", - "weight": 0.040746 + "weight": 0.050664 }, { "from": "D", "to": "E", - "weight": 0.048858 + "weight": 0.045529 }, { "from": "D", "to": "G", - "weight": 0.071214 + "weight": 0.066863 }, { "from": "D", @@ -7528,12 +7578,12 @@ { "from": "D", "to": "I", - "weight": 0.061129 + "weight": 0.054875 }, { "from": "D", "to": "N", - "weight": 0.060418 + "weight": 0.065092 }, { "from": "D", @@ -7543,17 +7593,17 @@ { "from": "D", "to": "S", - "weight": 0.063491 + "weight": 0.064583 }, { "from": "D", "to": "T", - "weight": 0.087745 + "weight": 0.092883 }, { "from": "D", "to": "V", - "weight": 0.06298 + "weight": 0.052733 }, { "from": "D", @@ -7565,7 +7615,7 @@ { "from": "K", "to": "L", - "weight": 0.053225 + "weight": 0.063589 }, { "from": "K", @@ -7582,7 +7632,7 @@ { "from": "N", "to": "S", - "weight": 0.04573 + "weight": 0.0442 } ], "297": [ @@ -7594,17 +7644,22 @@ { "from": "V", "to": "L", - "weight": 0.021 + "weight": 0.033771 } ], "298": [ { "from": "N", "to": "H", - "weight": 0.0444 + "weight": 0.042733 } ], "299": [ + { + "from": "R", + "to": "H", + "weight": 0.0132 + }, { "from": "R", "to": "K", @@ -7618,7 +7673,7 @@ { "from": "R", "to": "P", - "weight": 0.0617 + "weight": 0.063627 }, { "from": "R", @@ -7640,7 +7695,7 @@ { "from": "I", "to": "A", - "weight": 0.04668 + "weight": 0.042017 }, { "from": "I", @@ -7660,7 +7715,7 @@ { "from": "I", "to": "W", - "weight": 0.025618 + "weight": 0.023925 } ], "301": [ @@ -7672,26 +7727,26 @@ { "from": "T", "to": "H", - "weight": 0.062 + "weight": 0.056614 }, { "from": "T", "to": "S", - "weight": 0.0227 + "weight": 0.0175 } ], "302": [ { "from": "Y", "to": "F", - "weight": 0.015967 + "weight": 0.02605 } ], "304": [ { "from": "A", "to": "D", - "weight": 0.030456 + "weight": 0.0437 }, { "from": "A", @@ -7701,17 +7756,17 @@ { "from": "A", "to": "H", - "weight": 0.029225 + "weight": 0.05946 }, { "from": "A", "to": "K", - "weight": 0.04142 + "weight": 0.037333 }, { "from": "A", "to": "L", - "weight": 0.047457 + "weight": 0.042075 }, { "from": "A", @@ -7721,22 +7776,22 @@ { "from": "A", "to": "N", - "weight": 0.04775 + "weight": 0.049375 }, { "from": "A", "to": "R", - "weight": 0.054229 + "weight": 0.053478 }, { "from": "A", "to": "S", - "weight": 0.050238 + "weight": 0.057213 }, { "from": "A", "to": "T", - "weight": 0.00995 + "weight": 0.013967 }, { "from": "A", @@ -7763,22 +7818,22 @@ { "from": "R", "to": "I", - "weight": 0.015457 + "weight": 0.013888 }, { "from": "R", "to": "K", - "weight": 0.045 + "weight": 0.047007 }, { "from": "R", "to": "L", - "weight": 0.050671 + "weight": 0.050022 }, { "from": "R", "to": "M", - "weight": 0.0412 + "weight": 0.03846 }, { "from": "R", @@ -7793,12 +7848,12 @@ { "from": "R", "to": "S", - "weight": 0.05448 + "weight": 0.051483 }, { "from": "R", "to": "T", - "weight": 0.0256 + "weight": 0.047033 }, { "from": "R", @@ -7813,43 +7868,43 @@ { "from": "R", "to": "Y", - "weight": 0.0569 + "weight": 0.054625 } ], "308": [ { "from": "Y", "to": "F", - "weight": 0.035638 + "weight": 0.032489 } ], "309": [ { "from": "V", "to": "I", - "weight": 0.058177 + "weight": 0.056686 } ], "310": [ { "from": "K", "to": "H", - "weight": 0.030333 + "weight": 0.049575 }, { "from": "K", "to": "I", - "weight": 0.044557 + "weight": 0.03915 }, { "from": "K", "to": "L", - "weight": 0.0697 + "weight": 0.072055 }, { "from": "K", "to": "N", - "weight": 0.0099 + "weight": 0.0264 }, { "from": "K", @@ -7864,19 +7919,19 @@ { "from": "K", "to": "V", - "weight": 0.02038 + "weight": 0.0239 } ], "311": [ { "from": "Q", "to": "A", - "weight": 0.0307 + "weight": 0.02668 }, { "from": "Q", "to": "C", - "weight": 0.064162 + "weight": 0.074221 }, { "from": "Q", @@ -7886,7 +7941,7 @@ { "from": "Q", "to": "K", - "weight": 0.06022 + "weight": 0.062133 }, { "from": "Q", @@ -7896,32 +7951,32 @@ { "from": "Q", "to": "M", - "weight": 0.040331 + "weight": 0.038888 }, { "from": "Q", "to": "R", - "weight": 0.0845 + "weight": 0.0781 }, { "from": "Q", "to": "S", - "weight": 0.028567 + "weight": 0.026957 }, { "from": "Q", "to": "T", - "weight": 0.019733 + "weight": 0.0278 }, { "from": "Q", "to": "V", - "weight": 0.026856 + "weight": 0.03576 }, { "from": "Q", "to": "W", - "weight": 0.0424 + "weight": 0.03995 }, { "from": "Q", @@ -7948,22 +8003,22 @@ { "from": "N", "to": "G", - "weight": 0.0509 + "weight": 0.047733 }, { "from": "N", "to": "K", - "weight": 0.044222 + "weight": 0.061745 }, { "from": "N", "to": "M", - "weight": 0.0197 + "weight": 0.027229 }, { "from": "N", "to": "P", - "weight": 0.033186 + "weight": 0.050922 }, { "from": "N", @@ -7973,22 +8028,22 @@ { "from": "N", "to": "R", - "weight": 0.052623 + "weight": 0.05898 }, { "from": "N", "to": "S", - "weight": 0.042744 + "weight": 0.048882 }, { "from": "N", "to": "T", - "weight": 0.0603 + "weight": 0.043417 }, { "from": "N", "to": "Y", - "weight": 0.048689 + "weight": 0.04504 } ], "313": [ @@ -8000,7 +8055,7 @@ { "from": "T", "to": "S", - "weight": 0.048933 + "weight": 0.046819 } ], "314": [ @@ -8012,19 +8067,19 @@ { "from": "L", "to": "M", - "weight": 0.039683 + "weight": 0.039343 } ], "315": [ { "from": "K", "to": "L", - "weight": 0.140019 + "weight": 0.143082 }, { "from": "K", "to": "M", - "weight": 0.0655 + "weight": 0.071778 }, { "from": "K", @@ -8041,7 +8096,7 @@ { "from": "T", "to": "L", - "weight": 0.055829 + "weight": 0.056389 }, { "from": "T", @@ -8051,7 +8106,7 @@ { "from": "T", "to": "V", - "weight": 0.049656 + "weight": 0.050429 } ], "320": [ @@ -8065,32 +8120,32 @@ { "from": "V", "to": "C", - "weight": 0.061523 + "weight": 0.060929 }, { "from": "V", "to": "F", - "weight": 0.068631 + "weight": 0.07382 }, { "from": "V", "to": "H", - "weight": 0.03018 + "weight": 0.032758 }, { "from": "V", "to": "I", - "weight": 0.054386 + "weight": 0.0621 }, { "from": "V", "to": "K", - "weight": 0.057068 + "weight": 0.077757 }, { "from": "V", "to": "L", - "weight": 0.055762 + "weight": 0.06732 }, { "from": "V", @@ -8100,12 +8155,12 @@ { "from": "V", "to": "N", - "weight": 0.038773 + "weight": 0.046106 }, { "from": "V", "to": "R", - "weight": 0.056983 + "weight": 0.074456 }, { "from": "V", @@ -8115,24 +8170,24 @@ { "from": "V", "to": "T", - "weight": 0.05735 + "weight": 0.053638 }, { "from": "V", "to": "W", - "weight": 0.042192 + "weight": 0.049429 }, { "from": "V", "to": "Y", - "weight": 0.01536 + "weight": 0.016017 } ], "324": [ { "from": "P", "to": "A", - "weight": 0.056573 + "weight": 0.065846 }, { "from": "P", @@ -8147,22 +8202,22 @@ { "from": "P", "to": "M", - "weight": 0.084936 + "weight": 0.082694 }, { "from": "P", "to": "N", - "weight": 0.052977 + "weight": 0.059 }, { "from": "P", "to": "Q", - "weight": 0.04077 + "weight": 0.049417 }, { "from": "P", "to": "R", - "weight": 0.03745 + "weight": 0.036044 } ], "325": [ @@ -8174,14 +8229,14 @@ { "from": "E", "to": "S", - "weight": 0.038283 + "weight": 0.039014 } ], "326": [ { "from": "K", "to": "A", - "weight": 0.0442 + "weight": 0.04812 }, { "from": "K", @@ -8196,7 +8251,7 @@ { "from": "K", "to": "I", - "weight": 0.030329 + "weight": 0.030433 }, { "from": "K", @@ -8206,7 +8261,7 @@ { "from": "K", "to": "M", - "weight": 0.043078 + "weight": 0.040218 }, { "from": "K", @@ -8236,24 +8291,24 @@ { "from": "K", "to": "W", - "weight": 0.03862 + "weight": 0.0457 }, { "from": "K", "to": "Y", - "weight": 0.03675 + "weight": 0.08396 } ], "327": [ { "from": "Q", "to": "A", - "weight": 0.05754 + "weight": 0.0492 }, { "from": "Q", "to": "E", - "weight": 0.03252 + "weight": 0.036183 }, { "from": "Q", @@ -8278,19 +8333,19 @@ { "from": "Q", "to": "T", - "weight": 0.042592 + "weight": 0.0395 } ], "328": [ { "from": "T", "to": "A", - "weight": 0.051844 + "weight": 0.04818 }, { "from": "T", "to": "F", - "weight": 0.049959 + "weight": 0.064521 }, { "from": "T", @@ -8300,7 +8355,7 @@ { "from": "T", "to": "M", - "weight": 0.053971 + "weight": 0.056293 }, { "from": "T", @@ -8325,14 +8380,14 @@ { "from": "T", "to": "Y", - "weight": 0.051486 + "weight": 0.053706 } ], "329": [ { "from": "R", "to": "K", - "weight": 0.039813 + "weight": 0.040676 } ] } From 9c619a201bc4ee86cec88c720cee1b14d583472c Mon Sep 17 00:00:00 2001 From: John Huddleston Date: Wed, 17 Jan 2024 16:39:24 -0800 Subject: [PATCH 3/3] Only find Welsh epitope distances in nextflu-private workflow --- config/distance_maps.tsv | 2 - .../nextflu-private/antigenic_distances.smk | 39 +++++++++++++++++++ 2 files changed, 39 insertions(+), 2 deletions(-) diff --git a/config/distance_maps.tsv b/config/distance_maps.tsv index ab3c961e..18f4b8d0 100644 --- a/config/distance_maps.tsv +++ b/config/distance_maps.tsv @@ -3,8 +3,6 @@ h3n2 ha root ep wolf h3n2 ha root ne wolf_nonepitope h3n2 ha root rb koel h3n2 ha ancestor ne_star luksza_nonepitope -h3n2 ha root welsh_ep welsh_epitope_sites -h3n2 ha root welsh_escape welsh_escape_by_site_and_amino_acid h3n2 na root ep bhatt h3n2 na root ne bhatt_nonepitope h1n1pdm ha root ep canton diff --git a/profiles/nextflu-private/antigenic_distances.smk b/profiles/nextflu-private/antigenic_distances.smk index 531cbf1b..518ae8d4 100644 --- a/profiles/nextflu-private/antigenic_distances.smk +++ b/profiles/nextflu-private/antigenic_distances.smk @@ -112,6 +112,41 @@ rule scores: --output {output} """ +rule welsh_epitope_distances: + input: + tree = rules.refine.output.tree, + translations_done = build_dir + "/{build_name}/{segment}/translations.done", + distance_maps = [ + "config/distance_maps/h3n2/ha/welsh_epitope_sites.json", + "config/distance_maps/h3n2/ha/welsh_escape_by_site_and_amino_acid.json", + ], + output: + distances = "builds/{build_name}/{segment}/welsh_epitope_distances.json", + params: + alignments = lambda w: [f"{build_dir}/{w.build_name}/{w.segment}/nextalign/masked.gene.{gene}_withInternalNodes.fasta" for gene in GENES[w.segment]], + genes = lambda w: GENES[w.segment], + comparisons = ["root", "root"], + attribute_names = ["welsh_ep", "welsh_escape"], + conda: "../../workflow/envs/nextstrain.yaml" + benchmark: + "benchmarks/welsh_epitope_distances_{build_name}_{segment}.txt" + log: + "logs/welsh_epitope_distances_{build_name}_{segment}.txt" + resources: + mem_mb=8000, + time="00:30:00", + shell: + """ + augur distance \ + --tree {input.tree} \ + --alignment {params.alignments} \ + --gene-names {params.genes} \ + --compare-to {params.comparisons} \ + --attribute-name {params.attribute_names} \ + --map {input.distance_maps} \ + --output {output.distances} 2>&1 | tee {log} + """ + def get_private_node_data(wildcards): node_data = [ "builds/{build_name}/{segment}/scores.json", @@ -124,6 +159,10 @@ def get_private_node_data(wildcards): node_data.append(f"builds/{wildcards.build_name}/{wildcards.segment}/haplotypes_without_references/{collection['name']}.json") node_data.append(rules.titer_tree_cross_immunities.output.cross_immunities.format(titer_collection=collection["name"], **wildcards)) + # Only annotate Welsh epitope distances for H3N2 HA builds. + if "h3n2" in wildcards.build_name and wildcards.segment == "ha": + node_data.append(f"builds/{wildcards.build_name}/{wildcards.segment}/welsh_epitope_distances.json") + return node_data rule export_private: