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updatedhw1.txt
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updatedhw1.txt
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Which variants are present in which samples?
In SRR2584403, theres a variant at position 1329520 with reference allele T and alternate allele G. And a variant at position 4141016 with reference allele C and alternate allele A.
In SRR2584404, theres a variant at position 238917 with reference allele G and alternate allele T. A variant at position 806308 with reference allele ATT and alternate allele AT. A variant at position 1329520 with reference allele T and alternate allele G. And a variant at position 4141016 with reference allele C and alternate allele A.
In SRR2584405, theres a variant at position 649522 with reference allele C and alternate allele T. A variant at position 708118 with reference allele T and alternate allele C. A variant at position 1733754 with reference allele A and alternate allele T. A variant at position 2103887 with reference allele ACAGCCAGCCAGCCAGCCAGCCAGCCAGCCAG and alternate allele ACAGCCAGCCAGCCAGCCAGCCAGCCAGCCAGCCAG. And a variant at position 3762120 with reference allele C and alternate allele A.
In SRR2584857_1, theres a variant at position 920514 with reference allele T and alternate allele C. A variant at position 3931002 with reference allele A and alternate allele C. A variant at position 4141441 with reference allele C and alternate allele T. A variant at position 4202391 with reference allele T and alternate allele G. And a variant at position 4530767 with reference allele CACCCTAACCCT and alternate allele CACCCTAACCCTAACCCT.
In SRR2584857_2, theres a variant at position 920514 with reference allele T and alternate allele C. A variant at position 3901402 with reference allele G and alternate allele A. A variant at position 3931002 with reference allele A and alternate allele C. A variant at position 4141441 with reference allele C and alternate allele T. A variant at position 4202391 with reference allele T and alternate allele G. And a variant at position 4530767 with reference allele CACCCTAACCCT and alternate allele CACCCTAACCCTAACCCT.
Which variants are shared between one or more samples?
03 and 04 share a variant at 4141016 and at 1329520.
Which genes contain variants in more than one sample (and in which samples)?
03 and 04 share a variant at 4141016 which is in gene fabR. And 03 and 04 share a variant at 1329520 which is in gene topA.
Of the variants that are in a coding region, which are synonymous and which are non-synonymous? (Pick four genes of interest.)
Variant at position 2103887 (gene ECB_RS23820):
Synonymous: No
Variant at position 4530767 (gene gntP):
Synonymous: No
Variant at position 3762120 (gene spoT):
Synonymous: Yes
Variant at position 4202391 (gene iclR):
Synonymous: Yes