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Old 09-28-2016, 07:57 PM   #1
Rangika
Junior Member
 
Location: Sri Lanka

Join Date: Aug 2016
Posts: 6
Question Low coverage after alignment

Hi,

I'm working with a illumina Miseq 2*300bp PE 8 sample library run on a single lane of a flowcell. Ref ~32Mbp in size. I aligned PE raw dataset for one sample against the reference sequence using BWA-mem and checked mapping statistics using Picard CollectAlignmentSummaryMetrics and CollectRawWgsMetrics. Some of the results are as below.

GENOME_TERRITORY 32444968
MEAN_COVERAGE 19.467972
SD_COVERAGE 82.993179
MEDIAN_COVERAGE 17

output file from CollectAlignmentSummaryMetrics is also attached which shows that PCT_PF_READS_ALIGNED ~97% PF_HQ_ALIGNED_READS ~92% which I believe is good. But I'm confused with ~19% mean coverage. When I trim data I get a alignment with same quality but coverage is low as in the above case.

Can anybody give me any comments on this? Am I on the right track?

Thanks
Regards
Rangi
Attached Files
File Type: txt output_L2339.txt (2.3 KB, 5 views)
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