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result_report.Rmd
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result_report.Rmd
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---
title: "Variant calling quality control report"
output: html_document
params:
outdir: "../jx_240518_mix2/result2"
primer_file: "../jx_240518_mix2/primers_addGC.fa"
gene_file: "../jx_240518_mix2/gene_list.txt"
---
## 原始数据质量控制
测序得到下机序列数据为FASTQ格式,如同以下样子:
```
@EAS139:136:FC706VJ:2:2104:15343:197393 1:Y:18:ATCACG
GATTTGGGGTTCAAAGCAGTATCGATCAAATAGTAAATCCATTTGTTCAACTCACAGTTT
+
CCCCCGGGG#9BB<DFGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGFFGFFFFGG
```
第一行是一长串序列编号,记录了测序序列的一些信息;第二行是序列,为测序得到的ATCGN碱基信息;第三行是分隔符加号;第四行是对应测序碱基的质量分数,质量分数通过ASCII编码转换为字符串,方便记录和代码计算。如下是对应ASCII字符与质量分数的对应关系。
```
!"#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHIJ
0.2......................26...31........41
```
质量分数Q是对应碱基检测出错概率p的一个对应数字,对应公式如下:
\[
Q = -10 Log_{10}^p