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| # a read spans the reference position (starts before or at this reference position and ends at or after this position) | | # a read spans the reference position (starts before or at this reference position and ends at or after this position) |
| # 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) | + | # if CIGAR for this position is M/X/=/D/N (any cigar other than clip or insert) |
| *TotalReads - # of reads that span this position. | | *TotalReads - # of reads that span this position. |
− | *DupRate(%) - # of reads marked duplicate in the flag / TotalReads | + | *Dups - # of reads marked duplicate in the flag |
− | *QCFailRate(%) - # of reads marked QC failure in the flag / TotalReads | + | *QCFail - # of reads marked QC failure in the flag |
− | *PairedReads(%) - # of reads marked paired in the flag / TotalReads
| |
− | *ProperPaired(%) - # of reads marked paired AND proper paired in the flag / TotalReads
| |
− | *MappedBases - # of reads marked mapped in the flag
| |
− | *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
| |
− | *MapQual<10(%) - # of reads marked mapped in the flag AND have a Mapping Quality < 10 / TotalReads
| |
− | *MapRate_MQpass(%) - # of reads marked mapped in the flag AND have a Mapping Quality >= a minimum Mapping Quality / TotalReads
| |
| | | |
| + | No further stats are incremented if the read is a duplicate, QC failure, or unmapped. |
| | | |
− | For each position, the following counts exclude:
| + | Additional counts incremented ONLY for mapped, non-duplicate, non-QC failure reads: |
− | # unmapped reads | + | *Mapped - # of reads marked mapped in the flag |
− | # duplicates | + | *Paired - # of reads marked paired in the flag |
− | # failed QC | + | *ProperPaired - # of reads marked paired AND proper paired in the flag |
− | # deletions/skips (only CIGAR M/X/= are included) | + | *ZeroMapQual - # of reads that have a Mapping Quality of 0 |
− | # MapQ below the min | + | *MapQual<10 - # of reads that have a Mapping Quality < 10 |
| + | *MapQual255 - # of reads that have a Mapping Quality = 255 |
| + | *PassMapQual - # of reads that have a Mapping Quality >= a minimum Mapping Quality (version 1.0, this includes mapping quality 255 reads). |
| + | |
| + | Additional values ONLY for mapped, mapping quality != 255, non-duplicate, non-QC failure reads: |
| + | *AverageMapQuality - average calculated by summing all mapping qualities that are included (as defined above) and dividing by the number of mapping qualities added. |
| + | *AverageMapQualCount - # of mapping qualities used to calculate AverageMapQuality. |
| + | |
| + | Additional values ONLY incremented for mapped, mapping quality >= min mapping quality, non-duplicate, non-QC failure reads (version 1.0, this includes mapping quality 255 reads): |
| *Depth - # of reads. | | *Depth - # of reads. |
| *Q20Bases - # 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
| + | |
| + | Currently there is no special logic to exclude positions where the refernce is 'N'. |
| + | |
| + | Currently there is no special logic to exclude reads from the counts when the base is 'N'. |
| | | |
| | | |
− | For each position, the following counts exclude:
| + | === BaseQC Output === |
− | # unmapped reads
| + | There are two output options for BaseQC. |
− | # duplicates
| + | # Percentages |
− | # failed QC
| + | # Straight Counts |
− | # 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 positions where the refernce is 'N'.
| + | ==== Percentage-Based Output Format ==== |
| + | Order (with calculations based on the values described above): |
| + | *chrom - Chromosome/reference name string from the SAM/BAM |
| + | *chromStart - 0-based start position |
| + | *chromEnd - 0-based end position (always 1 greater than start and not included in this region) |
| + | *Depth - Depth |
| + | *Q20Bases - Q20Bases |
| + | *Q20BasesPct(%) - Q20Bases / Depth |
| + | *TotalReads - TotalReads |
| + | *MappedBases - Mapped |
| + | *MappingRate(%) - Mapped / TotalReads |
| + | *MapRate_MQPass(%) - PassMapQual / TotalReads |
| + | *ZeroMapQual(%) - ZeroMapQual / TotalReads |
| + | *MapQual<10(%) - MapQual<10 / TotalReads |
| + | *PairedReads(%) - Paired / TotalReads |
| + | *ProperPaired(%) - ProperPaired / TotalReads |
| + | *DupRate(%) - Dups / TotalReads |
| + | *QCFailRate(%) - QCFail / TotalReads |
| + | *AverageMapQuality - AverageMapQuality |
| + | *AverageMapQualCount - AverageMapQualCount |
| | | |
− | Currently there is no special logic to exclude reads from the counts when the base is 'N'.
| + | This output does not include a MapQual255 count in version 1.0. |
| | | |
| | | |
− | === Output Format === | + | ==== Count-Based Output Format ==== |
− | Order: | + | Order (of values described above): |
| *chrom - Chromosome/reference name string from the SAM/BAM | | *chrom - Chromosome/reference name string from the SAM/BAM |
| *chromStart - 0-based start position | | *chromStart - 0-based start position |
| *chromEnd - 0-based end position (always 1 greater than start and not included in this region) | | *chromEnd - 0-based end position (always 1 greater than start and not included in this region) |
− | *Depth - excludes unmapped reads, duplicates, failed QC, deletions/skips (only CIGAR M/X/= are included), MapQ below the min | + | *TotalReads |
− | *Q20Bases - excludes unmapped reads, duplicates, failed QC, deletions/skips (only CIGAR M/X/= are included), MapQ below the min
| + | *Dups |
− | *Q20BasesPct(%) - excludes unmapped reads, duplicates, failed QC, deletions/skips (only CIGAR M/X/= are included), MapQ below the min | + | *QCFail |
− | *TotalReads - only excludes clips | + | *Mapped |
− | *MappedBases - only excludes clips | + | *Paired |
− | *MappingRate(%) - only excludes clips | + | *ProperPaired |
− | *MapRate_MQPass(%) - only excludes clips | + | *ZeroMapQual |
− | *ZeroMapQual(%) - only excludes clips | + | *MapQual<10 |
− | *MapQual<10(%) - only excludes clips | + | *MapQual255 |
− | *PairedReads(%) - only excludes clips | + | *PassMapQual |
− | *ProperPaired(%) - only excludes clips | + | *AverageMapQuality |
− | *DupRate(%) - only excludes clips | + | *AverageMapQualCount |
− | *QCFailRate(%) - only excludes clips | + | *Depth |
− | *AverageMapQuality - excludes unmapped reads, duplicates, failed QC, deletions/skips (only CIGAR M/X/= are included), MapQ 255 | + | *Q20Bases |
− | *AverageMapQualCount - excludes unmapped reads, duplicates, failed QC, deletions/skips (only CIGAR M/X/= are included), MapQ 255 | + | |
| | | |
| === Sample Output === | | === Sample Output === |