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Update 07_qc_fastqc_assessment.md
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mistrm82 authored Apr 2, 2024
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Expand Up @@ -90,7 +90,14 @@ This plot can alert us to whether there were any problems occuring during sequen
<img src="../img/FastQC_seq_qual.png">
</p>

For example, the box plot at nucleotide 1 shows the distribution of quality scores for **the first nucleotide of all reads** in the `Mov10_oe_1` sample. The yellow box represents the 25th and 75th percentiles, with the red line as the median. The whiskers are the 10th and 90th percentiles. The blue line represents the average quality score for the nucleotide. Based on these metrics, the quality scores for the first nucleotide are quite high, with nearly all reads having scores above 28.
For example, the **box plot** at nucleotide 1 shows **the distribution of quality scores for the first nucleotide of all reads** in the `Mov10_oe_1` sample.

* The yellow box represents the 25th and 75th percentiles.
* The red line is the median value.
* The whiskers are the 10th and 90th percentiles.
* The blue line represents the average quality score for the nucleotide.

Based on these metrics, the quality scores for the first nucleotide are quite high, with nearly all reads having scores above 28.

The quality scores appear to drop going from the beginning toward the end of the reads. For reads generated by Illumina sequencing, this is not alarming and there are known causes for this drop in quality.

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