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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 |
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| | | |
| | | |
− | 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. |
| + | |
| | | |
| | | |
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| | | |
| 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> |