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| {|border=1 | | {|border=1 |
− | ! Field !! Description !!style="width: 80px"| Excludes Duplicates, QC Failures !!style="width: 80px"| Excludes Unmapped !!style="width: 80px"| Excludes MapQual = 255 !!style="width: 80px"| Excludes Below Min MapQual | + | ! Field !! Description !!style="width: 80px"| Excludes Duplicates, QC Failures !!style="width: 80px"| Excludes Unmapped !!style="width: 80px"| Excludes MapQual = 255 !!style="width: 80px"| Excludes Below Min MapQual !!style="width: 80px"| Excludes CIGAR Deletions, Skips |
| |- | | |- |
| | chrom || Chromosome/reference name string from the SAM/BAM | | | chrom || Chromosome/reference name string from the SAM/BAM |
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| | 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 || # of reads that are mapped with acceptable Mapping Quality, and are not duplicates or QC failures || align="center"|X || align="center"|X || || align="center"|X | + | | Depth || # of reads that are mapped with acceptable Mapping Quality, and are not duplicates or QC failures || align="center"|X || align="center"|X || || align="center"|X || align="center"|X |
| |- | | |- |
− | | Q20Bases || # of bases at this position with a base quality (from the read) of Q20 or higher || align="center"|X || align="center"|X || || align="center"|X | + | | Q20Bases || # of bases at this position with a base quality (from the read) of Q20 or higher || align="center"|X || align="center"|X || || align="center"|X || align="center"|X |
| |- | | |- |
− | | Q20BasesPct(%) || Q20Bases / Depth || align="center"|X || align="center"|X || || align="center"|X | + | | Q20BasesPct(%) || Q20Bases / Depth || align="center"|X || align="center"|X || || align="center"|X || align="center"|X |
| |- | | |- |
− | | TotalReads || # of reads that span this position || || || || | + | | TotalReads || # of reads that span this position || || || || || |
| |- | | |- |
− | | MappedBases || # of reads marked mapped in the flag || align="center"|X || align="center"|X || || | + | | MappedBases || # of reads marked mapped in the flag || align="center"|X || align="center"|X || || || |
| |- | | |- |
− | | MappingRate(%) || MappedBases / TotalReads || align="center"|X || align="center"|X || || | + | | MappingRate(%) || MappedBases / TotalReads || align="center"|X || align="center"|X || || || |
| |- | | |- |
− | | MapRate_MQPass(%) || # of reads that have a Mapping Quality >= a minimum Mapping Quality / TotalReads || align="center"|X || align="center"|X || || | + | | MapRate_MQPass(%) || # of reads that have a Mapping Quality >= a minimum Mapping Quality / TotalReads || align="center"|X || align="center"|X || || || |
| |- | | |- |
− | | ZeroMapQual(%) || # of reads that have a Mapping Quality of 0 / TotalReads || align="center"|X || align="center"|X || || | + | | ZeroMapQual(%) || # of reads that have a Mapping Quality of 0 / TotalReads || align="center"|X || align="center"|X || || || |
| |- | | |- |
− | | MapQual<10(%) || # of reads that have a Mapping Quality < 10 / TotalReads || align="center"|X || align="center"|X || || | + | | MapQual<10(%) || # of reads that have a Mapping Quality < 10 / TotalReads || align="center"|X || align="center"|X || || || |
| |- | | |- |
− | | PairedReads(%) || # of reads marked paired in the flag / TotalReads || align="center"|X || align="center"|X || || | + | | PairedReads(%) || # of reads marked paired in the flag / TotalReads || align="center"|X || align="center"|X || || || |
| |- | | |- |
− | | ProperPaired(%) || # of reads marked paired AND proper paired in the flag / TotalReads || align="center"|X || align="center"|X || || | + | | ProperPaired(%) || # of reads marked paired AND proper paired in the flag / TotalReads || align="center"|X || align="center"|X || || || |
| |- | | |- |
− | | 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 || || || || || |
| |- | | |- |
− | | AverageMapQuality || sum of included mapping qualities / AverageMapQualCount || align="center"|X || align="center"|X || align="center"|X || | + | | AverageMapQuality || sum of included mapping qualities / AverageMapQualCount || align="center"|X || align="center"|X || align="center"|X || || |
| |- | | |- |
− | | AverageMapQualCount || # of mapping qualities in AverageMapQuality || align="center"|X || align="center"|X || align="center"|X || | + | | AverageMapQualCount || # of mapping qualities in AverageMapQuality || align="center"|X || align="center"|X || align="center"|X || || |
| |- | | |- |
| |} | | |} |
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| Order/Descriptions: | | Order/Descriptions: |
| {|border=1 | | {|border=1 |
− | ! Field !! Description !!style="width: 80px"| Excludes Duplicates, QC Failures !!style="width: 80px"| Excludes Unmapped !!style="width: 80px"| Excludes MapQual = 255 !!style="width: 80px"| Excludes Below Min MapQual | + | ! Field !! Description !!style="width: 80px"| Excludes Duplicates, QC Failures !!style="width: 80px"| Excludes Unmapped !!style="width: 80px"| Excludes MapQual = 255 !!style="width: 80px"| Excludes Below Min MapQual !!style="width: 80px"| Excludes CIGAR Deletions, Skips |
| |- | | |- |
| | chrom || Chromosome/reference name string from the SAM/BAM | | | chrom || Chromosome/reference name string from the SAM/BAM |
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| | 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) |
| |- | | |- |
− | | TotalReads || # of reads that span this position || || || || | + | | TotalReads || # of reads that span this position || || || || || |
| |- | | |- |
− | | Dups || # of reads marked duplicate in the flag || || || || | + | | Dups || # of reads marked duplicate in the flag || || || || || |
| |- | | |- |
− | | QCFail || # of reads marked QC failure in the flag || || || || | + | | QCFail || # of reads marked QC failure in the flag || || || || || |
| |- | | |- |
− | | Mapped || # of reads marked mapped in the flag || align="center"|X || align="center"|X || || | + | | Mapped || # of reads marked mapped in the flag || align="center"|X || align="center"|X || || || |
| |- | | |- |
− | | Paired || # of reads marked paired in the flag || align="center"|X || align="center"|X || || | + | | Paired || # of reads marked paired in the flag || align="center"|X || align="center"|X || || || |
| |- | | |- |
− | | ProperPaired || # of reads marked paired AND proper paired in the flag || align="center"|X || align="center"|X || || | + | | ProperPaired || # of reads marked paired AND proper paired in the flag || align="center"|X || align="center"|X || || || |
| |- | | |- |
− | | ZeroMapQual || # of reads that have a Mapping Quality of 0 || align="center"|X || align="center"|X || || | + | | ZeroMapQual || # of reads that have a Mapping Quality of 0 || align="center"|X || align="center"|X || || || |
| |- | | |- |
− | | MapQual<10(%) || # of reads that have a Mapping Quality < 10 || align="center"|X || align="center"|X || || | + | | MapQual<10(%) || # of reads that have a Mapping Quality < 10 || align="center"|X || align="center"|X || || || |
| |- | | |- |
− | | MapQual255 || # of reads that have a Mapping Quality = 255 || align="center"|X || align="center"|X || || | + | | MapQual255 || # of reads that have a Mapping Quality = 255 || align="center"|X || align="center"|X || || || |
| |- | | |- |
− | | PassMapQual || # of reads that have a Mapping Quality >= a minimum Mapping Quality || align="center"|X || align="center"|X || || | + | | PassMapQual || # of reads that have a Mapping Quality >= a minimum Mapping Quality || align="center"|X || align="center"|X || || || |
| |- | | |- |
− | | AverageMapQuality || sum of included mapping qualities / AverageMapQualCount || align="center"|X || align="center"|X || align="center"|X || | + | | AverageMapQuality || sum of included mapping qualities / AverageMapQualCount || align="center"|X || align="center"|X || align="center"|X || || |
| |- | | |- |
| | AverageMapQualCount || # of mapping qualities in AverageMapQuality || align="center"|X || align="center"|X || align="center"|X || | | | AverageMapQualCount || # of mapping qualities in AverageMapQuality || align="center"|X || align="center"|X || align="center"|X || |
| + | |- || |
| + | | Depth || # of reads that are mapped with acceptable Mapping Quality, and are not duplicates or QC failures || align="center"|X || align="center"|X || || align="center"|X || align="center"|X |
| |- | | |- |
− | | Depth || # of reads that are mapped with acceptable Mapping Quality, and are not duplicates or QC failures || align="center"|X || align="center"|X || || align="center"|X
| + | | Q20Bases || # of bases at this position with a base quality (from the read) of Q20 or higher || align="center"|X || align="center"|X || || align="center"|X || align="center"|X |
− | |-
| |
− | | Q20Bases || # of bases at this position with a base quality (from the read) of Q20 or higher || align="center"|X || align="center"|X || || align="center"|X | |
| |- | | |- |
| |} | | |} |