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# regardless of duplicate/qc failure/unmapped/mapping quality
# regardless of duplicate/qc failure/unmapped/mapping quality
# regardless of the CIGAR for this position (other than clips at the beginning/end which are not counted, but deletions and skips are counted)
# regardless of the CIGAR for this position (other than clips at the beginning/end which are not counted, but deletions and skips are counted)
*TotalReads(e6) - # of reads that span this position.
*TotalReads - # of reads that span this position.
*DupRate(%) - # of reads marked duplicate in the flag / TotalReads
*DupRate(%) - # of reads marked duplicate in the flag / TotalReads
*QCFailRate(%) - # of reads marked QC failure in the flag / TotalReads
*QCFailRate(%) - # of reads marked QC failure in the flag / TotalReads
*PairedReads(%) - # of reads marked paired in the flag / TotalReads
*PairedReads(%) - # of reads marked paired in the flag / TotalReads
*ProperPaired(%) - # of reads marked paired AND proper paired in the flag / TotalReads
*ProperPaired(%) - # of reads marked paired AND proper paired in the flag / TotalReads
*MappedBases(e9) - # of reads marked mapped in the flag
*MappedBases - # of reads marked mapped in the flag
*MappingRate(%) - # of reads marked mapped in the flag / TotalReads
*MappingRate(%) - # of reads marked mapped in the flag / TotalReads
*ZeroMapQual(%) - # of reads marked mapped in the flag AND have a Mapping Quality of 0 / TotalReads
*ZeroMapQual(%) - # of reads marked mapped in the flag AND have a Mapping Quality of 0 / TotalReads
For each position, the following counts are incremented if:
For each position, the following counts exclude:
# a read spans the reference position (starts before or at this reference position and ends at or after this position)
# unmapped reads
# the read is NOT a duplicate, qc failure, unmapped, or mapped with a mapping quality less than the min
# duplicates
# the CIGAR for this position is a M/=/X (match/mismatch)
# failed QC
# deletions/skips (only CIGAR M/X/= are included)
# MapQ below the min
*Depth - # of reads.
*Depth - # of reads.
*Q20Bases(e9) - # of bases at this position with a base quality (from the read) of Q20 or higher.
*Q20Bases - # of bases at this position with a base quality (from the read) of Q20 or higher.
*Q20BasesPct(%) - Q20Bases / Depth
*Q20BasesPct(%) - Q20Bases / Depth
For each position, the following counts exclude:
# unmapped reads
# duplicates
# failed QC
# deletions/skips (only CIGAR M/X/= are included)
# MapQ of 255
*AverageMapQuality - average calculated by summing all mapping qualities that are not excluded (as defined above) and dividing by the number of mapping qualities added.
*AverageMapQualCount - # of mapping qualities used to calculate AverageMapQuality.
Currently there is no special logic to exclude reads from the counts when the base is 'N'.
Currently there is no special logic to exclude reads from the counts when the base is 'N'.
=== Sample Output ===
<pre>
chrom chromStart chromEnd Depth Q20Bases Q20BasesPct(%) TotalReads MappedBases MappingRate(%) MapRate_MQPass(%) ZeroMapQual(%) MapQual<10(%) PairedReads(%) ProperPaired(%) DupRate(%) QCFailRate(%) AverageMapQuality AverageMapQualCount
1 100 101 2 2 100.000 3 3 100.000 66.667 33.333 66.667 100.000 0.000 0.000 0.000 11.000 3
1 101 102 2 0 0.000 3 3 100.000 66.667 33.333 66.667 100.000 0.000 0.000 0.000 11.000 3
1 102 103 0 0 0.000 3 3 100.000 66.667 33.333 66.667 100.000 0.000 0.000 0.000 0.000 0
1 103 104 0 0 0.000 3 3 100.000 66.667 33.333 66.667 100.000 0.000 0.000 0.000 0.000 0
1 104 105 2 0 0.000 3 3 100.000 66.667 33.333 66.667 100.000 0.000 0.000 0.000 11.000 3
1 105 106 2 2 100.000 3 3 100.000 66.667 33.333 66.667 100.000 0.000 0.000 0.000 11.000 3
1 110 111 0 0 0.000 3 3 100.000 66.667 33.333 66.667 100.000 0.000 0.000 0.000 0.000 0
1 111 112 2 2 100.000 3 3 100.000 66.667 33.333 66.667 100.000 0.000 0.000 0.000 11.000 3
1 112 113 2 2 100.000 3 3 100.000 66.667 33.333 66.667 100.000 0.000 0.000 0.000 11.000 3
1 10012 10013 14 0 0.000 42 33 78.571 52.381 26.190 52.381 85.714 35.714 14.286 14.286 11.000 21
1 10013 10014 14 10 71.429 39 30 76.923 51.282 25.641 51.282 84.615 38.462 15.385 15.385 11.000 21
1 10023 10024 0 0 0.000 39 30 76.923 51.282 25.641 51.282 84.615 38.462 15.385 15.385 0.000 0
1 10024 10025 14 12 85.714 39 30 76.923 51.282 25.641 51.282 84.615 38.462 15.385 15.385 11.000 21
</pre>
