ION Proton exome sequencing results (FASTQC report) - typical/OK quality?

bybor · 03-28-2015, 05:14 AM

Hi

I have NGS exome sequencing results (fastq file) and I generated FASTQC report for it, and AFAICS the result looks like sequencing data is suboptimal. I am alien to the field, and would like to get community's opinion on how good/bad/typical the data actually is.

The lab told they used Ion Proton and followed ACMG standards - no more details, don't know chemistry kit.

The report below, and thanks in advance.

FASTQC version 0.11.2
File type: Conventional base calls
Encoding: Sanger / Illumina 1.9
Total Sequences: 33803990
Sequences flagged as poor quality: 0
Sequence length: 8-376
%GC: 48

Per base sequence quality, Error icon

Per sequence quality scores, Warning icon

Per base sequence content, Error icon

Per sequence GC content, Warning icon

Per base N content, OK icon

Sequence Length Distribution, Warning icon

Sequence Duplication Levels, OK icon

Overrepresented sequences, OK icon
No overrepresented sequences

Adapter Content, OK icon

Kmer Content, Error icon

GenoMax · 03-28-2015, 06:51 AM

See this thread for additional information about Q-scores on Ion platform: http://seqanswers.com/forums/showthread.php?t=33555

Your data may be of good quality based on the discussion in thread above.

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03-28-2015, 05:14 AM	#1
bybor Junior Member Location: Russia Join Date: Mar 2015 Posts: 3	ION Proton exome sequencing results (FASTQC report) - typical/OK quality? Hi I have NGS exome sequencing results (fastq file) and I generated FASTQC report for it, and AFAICS the result looks like sequencing data is suboptimal. I am alien to the field, and would like to get community's opinion on how good/bad/typical the data actually is. The lab told they used Ion Proton and followed ACMG standards - no more details, don't know chemistry kit. The report below, and thanks in advance. FASTQC version 0.11.2 File type: Conventional base calls Encoding: Sanger / Illumina 1.9 Total Sequences: 33803990 Sequences flagged as poor quality: 0 Sequence length: 8-376 %GC: 48 Per base sequence quality, Error icon Per sequence quality scores, Warning icon Per base sequence content, Error icon Per sequence GC content, Warning icon Per base N content, OK icon Sequence Length Distribution, Warning icon Sequence Duplication Levels, OK icon Overrepresented sequences, OK icon No overrepresented sequences Adapter Content, OK icon Kmer Content, Error icon

03-28-2015, 06:51 AM	#2
GenoMax Senior Member Location: East Coast USA Join Date: Feb 2008 Posts: 7,080	See this thread for additional information about Q-scores on Ion platform: http://seqanswers.com/forums/showthread.php?t=33555 Your data may be of good quality based on the discussion in thread above.