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Old 03-28-2015, 05:14 AM   #1
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Location: Russia

Join Date: Mar 2015
Posts: 3
Default ION Proton exome sequencing results (FASTQC report) - typical/OK quality?


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

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Old 03-28-2015, 06:51 AM   #2
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Location: East Coast USA

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Posts: 7,080

See this thread for additional information about Q-scores on Ion platform:

Your data may be of good quality based on the discussion in thread above.
GenoMax is offline   Reply With Quote

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