PSOMAGEN NGS Report

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Appendix

Result File Description

Deliverables List

File Type	File Name	Description
[Sample name]_[read1].fastq.gz	Raw read1 sequence data
[Sample name]_[read2].fastq.gz	Raw read2 sequence data
md5sum	[Order#]_[#samples]_md5sum[_DownloadLink].txt	You can download this file by clicking on the "md5sum List" button found on the "Download List" page. The file is slightly different in terms content, depending on how you’re receiving your data. If you’re receiving via download link, the file contains the following information : File name, File size, md5sum, FTP link. Otherwise, if your receiving your data via HDD the file only contains : File name, File size, and md5sum. MD5 is a string of 32 hexadecimal values, which represents a 'fingerprint' of a file. By comparing the supplied MD5 value to the actual value computed by the MD5sums utility, you can make sure that the file that you downloaded off of the internet has not been tampered with or modified from the original file stored in our server.

FASTQ Format

Phred Quality Score

Phred quality score numerically expresses the accuracy of each nucleotide. Higher Q number signifies higher accuracy.
For example, if Phred assigns a quality score of 30 to a base, the chances of having base call error are 1 in 1000.
Phred Quality Score Q is calculated with -10log₁₀(P), where p is probability of erroneous base call.

Quality of phred score	Probability of incorrect base call	Base call accuracy
10	1 in 10	90%
20	1 in 100	99%
30	1 in 1000	99.9%
40	1 in 10000	99.99%

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	Order Number