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FastQC showed me my raw data has 2 peaks in the GC content tab

edited March 2018 in Ask the GATK team

Hello,

I just got my FFPE samples back from the sequence provider, I see a double peak like in the image, what does it mean? Should I be worried? Is this normal for FFPE samples? It was a single pair of normal/tumor samples.

Also, the fastQs for my matched normal is so much smaller at ~8GB than my tumor data ~40GB.

Here's the basic stats from the bam file after alignment and duplicate marking:
47803854 + 0 in total (QC-passed reads + QC-failed reads)
20972021 + 0 duplicates
24883875 + 0 mapped (52.05%:-nan%)
47803854 + 0 paired in sequencing
23901927 + 0 read1
23901927 + 0 read2
20554832 + 0 properly paired (43.00%:-nan%)
23992038 + 0 with itself and mate mapped
891837 + 0 singletons (1.87%:-nan%)
40520 + 0 with mate mapped to a different chr
32160 + 0 with mate mapped to a different chr (mapQ>=5)

212511606 + 0 in total (QC-passed reads + QC-failed reads)
22840440 + 0 duplicates
62720862 + 0 mapped (29.51%:-nan%)
212511606 + 0 paired in sequencing
106255803 + 0 read1
106255803 + 0 read2
43991506 + 0 properly paired (20.70%:-nan%)
58253560 + 0 with itself and mate mapped
4467302 + 0 singletons (2.10%:-nan%)
116068 + 0 with mate mapped to a different chr
77003 + 0 with mate mapped to a different chr (mapQ>=5)

Will my downstream analysis be okay? I'd appreciate any advice.

Answers

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