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BamUtil: stats (view source)

Revision as of 16:14, 7 October 2011

282 bytes added ,  16:14, 7 October 2011
add that deletions/skips are excluded from depth/q20 bases
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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
   
|-
 
|-
 
|}
 
|}
Retrieved from "http://genome.sph.umich.edu/wiki/Special:MobileDiff/3914"

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