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  • sam file total matched base and total bases

    I have a fasta, most of the sequence is from repeat region, so they can be mapped to reference in sam lots of times. I use bwa mem with "-a" option, so they appear many times in different position of reference. Now I want to calculate the total matched bases / total bases in the sam file. I use samtools stats result.sam, the report is below:

    # This file was produced by samtools stats (1.3.1+htslib-1.3.1) and can be plott
    ed using plot-bamstats
    # This file contains statistics for all reads.
    # The command line was: stats result.sam
    # CHK, Checksum [2]Read Names [3]Sequences [4]Qualities
    # CHK, CRC32 of reads which passed filtering followed by addition (32bit overflo
    w)
    CHK 8146bdfb 3b00f1ed 091ce229
    # Summary Numbers. Use `grep ^SN | cut -f 2-` to extract this part.
    SN raw total sequences: 961
    SN filtered sequences: 0
    SN sequences: 961
    SN is sorted: 0
    SN 1st fragments: 961
    SN last fragments: 0
    SN reads mapped: 961
    SN reads mapped and paired: 0 # paired-end technology bit set
    + both mates mapped
    SN reads unmapped: 0
    SN reads properly paired: 0 # proper-pair bit set
    SN reads paired: 0 # paired-end technology bit set
    SN reads duplicated: 0 # PCR or optical duplicate bit set
    SN reads MQ0: 384 # mapped and MQ=0
    SN reads QC failed: 0
    SN non-primary alignments: 24643
    SN total length: 4353396 # ignores clipping
    SN bases mapped: 4353396 # ignores clipping
    SN bases mapped (cigar): 4428969 # more accurate

    SN bases trimmed: 0
    SN bases duplicated: 0
    SN mismatches: 79181 # from NM fields
    SN error rate: 1.787798e-02 # mismatches / bases mapped (cigar)
    SN average length: 4530
    SN maximum length: 14146
    SN average quality: 255.0
    SN insert size average: 0.0
    SN insert size standard deviation: 0.0
    SN inward oriented pairs: 0
    SN outward oriented pairs: 0
    SN pairs with other orientation: 0
    SN pairs on different chromosomes: 0

    The total mapped bases(cigar) 4428969 is longer than the total length 4353396, because the my reads are mostly repeat? What is the total bases mean in the report? So if I want to get the ratio of total matched bases / total bases, do I need to analysis cigar myself ? I try picard, but it always report error though I validate the sam without error.

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