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  • Rangika
    Junior Member
    • Aug 2016
    • 6
    #1

    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
    Tags: coverage, mapping statistics.
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