Difference between revisions of "BamUtil: stats"

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[[Category:BamUtil|stats]]
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<br>
[[Category:BAM Software]]
 
[[Category:Software]]
 
  
= Overview of the <code>stats</code> function of <code>bamUtil</code> =
+
= Overview of the <code>stats</code> function of <code>bamUtil</code> =
The <code>stats</code> option on the [[bamUtil]] executable generates the specified statistics on a SAM/BAM file.
 
  
= Parameters =
+
The <code>stats</code> option on the [[BamUtil]] executable generates the specified statistics on a SAM/BAM file.
<pre>
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Required Parameters:
+
= Parameters =
--in : the SAM/BAM file to calculate stats for
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<pre> Required Parameters:
 +
--in&nbsp;: the SAM/BAM file to calculate stats for
 
Types of Statistics that can be generated:
 
Types of Statistics that can be generated:
--basic       : Turn on basic statistic generation
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--basic     &nbsp;: Turn on basic statistic generation
--qual       : Generate a count for each quality (displayed as non-phred quality)
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--qual       &nbsp;: Generate a count for each quality (displayed as non-phred quality)
--phred       : Generate a count for each quality (displayed as phred quality)
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--phred     &nbsp;: Generate a count for each quality (displayed as phred quality)
--baseQC     : Write per base statistics to the specified file.
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--baseQC     &nbsp;: Write per base statistics to the specified file.
 
Optional Parameters:
 
Optional Parameters:
--maxNumReads : Maximum number of reads to process
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--maxNumReads&nbsp;: Maximum number of reads to process
 
                Defaults to -1 to indicate all reads.
 
                Defaults to -1 to indicate all reads.
--unmapped   : Only process unmapped reads (requires a bamIndex file)
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--unmapped   &nbsp;: Only process unmapped reads (requires a bamIndex file)
--bamIndex   : The path/name of the bam index file
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--bamIndex   &nbsp;: The path/name of the bam index file
 
                (if required and not specified, uses the --in value + ".bai")
 
                (if required and not specified, uses the --in value + ".bai")
--regionList : File containing the region list chr<tab>start_pos<tab>end<pos>.
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--regionList &nbsp;: File containing the region list chr&lt;tab&gt;start_pos&lt;tab&gt;end&lt;pos&gt;.
 
                Positions are 0 based and the end_pos is not included in the region.
 
                Positions are 0 based and the end_pos is not included in the region.
 
                Uses bamIndex.
 
                Uses bamIndex.
--minMapQual : The minimum mapping quality for filtering reads in the baseQC stats.
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--minMapQual &nbsp;: The minimum mapping quality for filtering reads in the baseQC stats.
--dbsnp       : The dbSnp file of positions to exclude from baseQC analysis.
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--dbsnp     &nbsp;: The dbSnp file of positions to exclude from baseQC analysis.
--noeof       : Do not expect an EOF block on a bam file.
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--noeof     &nbsp;: Do not expect an EOF block on a bam file.
--params     : Print the parameter settings
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--params     &nbsp;: Print the parameter settings
</pre>
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</pre>  
 
+
For all types of statistics, the bam file used is specified by <code>--in</code>.  
For all types of statistics, the bam file used is specified by <code>--in</code>.
 
  
 
The optional parameters are also used for all types of statistics.  
 
The optional parameters are also used for all types of statistics.  
  
Usage:
+
Usage:  
<pre>
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<pre> ./bam stats --in &lt;inputFile&gt; [--basic] [--qual] [--phred] [--baseQC &lt;outputFileName&gt;] [--maxNumReads &lt;maxNum&gt;] [--unmapped] [--bamIndex &lt;bamIndexFile&gt;] [--regionList &lt;regFileName&gt;] [--minMapQual &lt;minMapQ&gt;] [--dbsnp &lt;dbsnpFile&gt;] [--noeof] [--params]
./bam stats --in <inputFile> [--basic] [--qual] [--phred] [--baseQC <outputFileName>] [--maxNumReads <maxNum>] [--unmapped] [--bamIndex <bamIndexFile>] [--regionList <regFileName>] [--minMapQual <minMapQ>] [--dbsnp <dbsnpFile>] [--noeof] [--params]
+
</pre>
</pre>
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<br>  
  
 +
= Types of Statistics  =
  
 +
== Basic  ==
  
= Types of Statistics =
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Prints summary statistics for the file:
  
== Basic ==
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*TotalReads - # of reads that are in the file  
Prints summary statistics for the file:
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*MappedReads - # of reads marked mapped in the flag  
*TotalReads - # of reads that are in the file
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*PairedReads - # of reads marked paired in the flag  
*MappedReads - # of reads marked mapped in the flag
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*ProperPair - # of reads marked paired AND proper paired in the flag  
*PairedReads - # of reads marked paired in the flag
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*DuplicateReads - # of reads marked duplicate in the flag  
*ProperPair - # of reads marked paired AND proper paired in the flag
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*QCFailureReads - # of reads marked QC failure in the flag  
*DuplicateReads - # of reads marked duplicate in the flag
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*MappingRate(%) - # of reads marked mapped in the flag / TotalReads  
*QCFailureReads - # of reads marked QC failure in the flag
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*PairedReads(%) - # of reads marked paired in the flag / TotalReads  
*MappingRate(%) - # of reads marked mapped in the flag / TotalReads
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*ProperPair(%) - # of reads marked paired AND proper paired in the flag / TotalReads  
*PairedReads(%) - # of reads marked paired in the flag / TotalReads
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*DupRate(%) - # of reads marked duplicate in the flag / TotalReads  
*ProperPair(%) - # of reads marked paired AND proper paired in the flag / TotalReads
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*QCFailRate(%) - # of reads marked QC failure in the flag / TotalReads  
*DupRate(%) - # of reads marked duplicate in the flag / TotalReads
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*TotalBases - # of bases in all reads  
*QCFailRate(%) - # of reads marked QC failure in the flag / TotalReads
 
*TotalBases - # of bases in all reads
 
 
*BasesInMappedReads - # of bases in reads marked mapped in the flag
 
*BasesInMappedReads - # of bases in reads marked mapped in the flag
  
== Qual/Phred ==
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== Qual/Phred ==
Prints a count of the number of times each quality value appears in the file.
 
*<code>phred</code> Displays Quality as phred integers [0-93]
 
*<code>qual</code>  Displays Quality as non-phred integers (phred + 33) [33-126]
 
  
 +
Prints a count of the number of times each quality value appears in the file.
  
== BaseQC ==
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*<code>phred</code> Displays Quality as phred integers [0-93]
 +
*<code>qual</code> Displays Quality as non-phred integers (phred + 33) [33-126]
  
The <code>baseQC</code> option generates the following statistics:
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<br>  
  
For each position, the following counts are incremented if:
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== BaseQC  ==
# 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
 
# if CIGAR for this position is M/X/=/D/N (any cigar other than clip or insert)
 
*TotalReads - # of reads that span this position.
 
*Dups - # of reads marked duplicate in the flag
 
*QCFail - # of reads marked QC failure in the flag
 
  
No further stats are incremented if the read is a duplicate, QC failure, or unmapped.
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The <code>baseQC</code> option generates the following statistics:
  
Additional counts incremented ONLY for mapped, non-duplicate, non-QC failure reads:
+
A read spans a position if the read starts at or before the position, ends at or after the position and the position is not a clip.  CIGAR operations allowed for the position are M/X/=/D/N.
*Mapped - # of reads marked mapped in the flag
 
*Paired - # of reads marked paired in the flag
 
*ProperPaired - # of reads marked paired AND proper paired in the flag
 
*ZeroMapQual - # of reads that have a Mapping Quality of 0
 
*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:
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Currently there is no special logic to exclude positions/reads where the reference base is 'N' or the read base is 'N'.  
*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):
+
<br>  
*Depth - # of reads. 
 
*Q20Bases - # of bases at this position with a base quality (from the read) of Q20 or higher.
 
  
Currently there is no special logic to exclude positions where the refernce is 'N'.
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=== BaseQC Output  ===
  
Currently there is no special logic to exclude reads from the counts when the base is 'N'.
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There are two output options for BaseQC.  
  
 +
#Percentages
 +
#Straight Counts
  
=== BaseQC Output ===
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==== Percentage-Based Output Format  ====
There are two output options for BaseQC.
 
# Percentages
 
# Straight Counts
 
  
==== Percentage-Based Output Format ====
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Order/Descriptions:  
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
 
  
This output does not include a MapQual255 count in version 1.0.
+
{|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
 +
|-
 +
| 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 || # 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
 +
|-
 +
| Q20BasesPct(%) || Q20Bases / Depth || align="center"|X || align="center"|X || || align="center"|X
 +
|-
 +
| TotalReads || # of reads that span this position || || || ||
 +
|-
 +
| MappedBases || # of reads marked mapped in the flag || align="center"|X || align="center"|X || ||
 +
|-
 +
| MappingRate(%) || MappedBases / TotalReads || align="center"|X || align="center"|X || ||
 +
|-
 +
| MapRate_MQPass(%) || # of reads that have a Mapping Quality &gt;= 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 || ||
 +
|-
 +
| MapQual&lt;10(%) || # of reads that have a Mapping Quality &lt; 10 / 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 || ||
 +
|-
 +
| DupRate(%) || # of reads marked duplicate 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 ||
 +
|-
 +
| AverageMapQualCount || # of mapping qualities in AverageMapQuality || align="center"|X || align="center"|X || align="center"|X ||
 +
|-
 +
|}
  
 +
This output does not include a MapQual255 count in version 1.0.
  
==== Count-Based Output Format ====
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===== Sample Output  =====
Order (of values described above):
+
<pre>chrom chromStart chromEnd Depth Q20Bases Q20BasesPct(%) TotalReads MappedBases MappingRate(%) MapRate_MQPass(%) ZeroMapQual(%) MapQual&lt;10(%) PairedReads(%) ProperPaired(%) DupRate(%) QCFailRate(%) AverageMapQuality AverageMapQualCount
*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)
 
*TotalReads
 
*Dups
 
*QCFail
 
*Mapped
 
*Paired
 
*ProperPaired
 
*ZeroMapQual
 
*MapQual<10
 
*MapQual255
 
*PassMapQual
 
*AverageMapQuality
 
*AverageMapQualCount
 
*Depth
 
*Q20Bases
 
 
 
 
 
=== 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
 
1 100 101 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
 
1 101 102 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
Line 168: Line 144:
 
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 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
 
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>
+
</pre>  
 +
==== Count-Based Output Format  ====
 +
 
 +
{|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
 +
|-
 +
| 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)
 +
|-
 +
| TotalReads || # of reads that span this position || || || ||
 +
|-
 +
| Dups || # of reads marked duplicate 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 || ||
 +
|-
 +
| 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 || ||
 +
|-
 +
| ZeroMapQual || # of reads that have a Mapping Quality of 0 || align="center"|X || align="center"|X || ||
 +
|-
 +
| MapQual&lt;10(%) || # of reads that have a Mapping Quality &lt; 10 || 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 &gt;= 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 ||
 +
|-
 +
| 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
 +
|-
 +
| 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
 +
|-
 +
|}
 +
 
 +
 
 +
 
 +
[[Category:BamUtil|stats]] [[Category:BAM_Software]] [[Category:Software]]

Revision as of 14:47, 7 October 2011


Overview of the stats function of bamUtil

The stats option on the BamUtil executable generates the specified statistics on a SAM/BAM file.

Parameters

	Required Parameters:
		--in : the SAM/BAM file to calculate stats for
	Types of Statistics that can be generated:
		--basic       : Turn on basic statistic generation
		--qual        : Generate a count for each quality (displayed as non-phred quality)
		--phred       : Generate a count for each quality (displayed as phred quality)
		--baseQC      : Write per base statistics to the specified file.
	Optional Parameters:
		--maxNumReads : Maximum number of reads to process
		                Defaults to -1 to indicate all reads.
		--unmapped    : Only process unmapped reads (requires a bamIndex file)
		--bamIndex    : The path/name of the bam index file
		                (if required and not specified, uses the --in value + ".bai")
		--regionList  : File containing the region list chr<tab>start_pos<tab>end<pos>.
		                Positions are 0 based and the end_pos is not included in the region.
		                Uses bamIndex.
		--minMapQual  : The minimum mapping quality for filtering reads in the baseQC stats.
		--dbsnp       : The dbSnp file of positions to exclude from baseQC analysis.
		--noeof       : Do not expect an EOF block on a bam file.
		--params      : Print the parameter settings

For all types of statistics, the bam file used is specified by --in.

The optional parameters are also used for all types of statistics.

Usage:

	./bam stats --in <inputFile> [--basic] [--qual] [--phred] [--baseQC <outputFileName>] [--maxNumReads <maxNum>] [--unmapped] [--bamIndex <bamIndexFile>] [--regionList <regFileName>] [--minMapQual <minMapQ>] [--dbsnp <dbsnpFile>] [--noeof] [--params]


Types of Statistics

Basic

Prints summary statistics for the file:

  • TotalReads - # of reads that are in the file
  • MappedReads - # of reads marked mapped in the flag
  • PairedReads - # of reads marked paired in the flag
  • ProperPair - # of reads marked paired AND proper paired in the flag
  • DuplicateReads - # of reads marked duplicate in the flag
  • QCFailureReads - # of reads marked QC failure in the flag
  • MappingRate(%) - # of reads marked mapped in the flag / TotalReads
  • PairedReads(%) - # of reads marked paired in the flag / TotalReads
  • ProperPair(%) - # of reads marked paired AND proper paired in the flag / TotalReads
  • DupRate(%) - # of reads marked duplicate in the flag / TotalReads
  • QCFailRate(%) - # of reads marked QC failure in the flag / TotalReads
  • TotalBases - # of bases in all reads
  • BasesInMappedReads - # of bases in reads marked mapped in the flag

Qual/Phred

Prints a count of the number of times each quality value appears in the file.

  • phred Displays Quality as phred integers [0-93]
  • qual Displays Quality as non-phred integers (phred + 33) [33-126]


BaseQC

The baseQC option generates the following statistics:

A read spans a position if the read starts at or before the position, ends at or after the position and the position is not a clip. CIGAR operations allowed for the position are M/X/=/D/N.

Currently there is no special logic to exclude positions/reads where the reference base is 'N' or the read base is 'N'.


BaseQC Output

There are two output options for BaseQC.

  1. Percentages
  2. Straight Counts

Percentage-Based Output Format

Order/Descriptions:

Field Description Excludes Duplicates, QC Failures Excludes Unmapped Excludes MapQual = 255 Excludes Below Min MapQual
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 # of reads that are mapped with acceptable Mapping Quality, and are not duplicates or QC failures X X X
Q20Bases # of bases at this position with a base quality (from the read) of Q20 or higher X X X
Q20BasesPct(%) Q20Bases / Depth X X X
TotalReads # of reads that span this position
MappedBases # of reads marked mapped in the flag X X
MappingRate(%) MappedBases / TotalReads X X
MapRate_MQPass(%) # of reads that have a Mapping Quality >= a minimum Mapping Quality / TotalReads X X
ZeroMapQual(%) # of reads that have a Mapping Quality of 0 / TotalReads X X
MapQual<10(%) # of reads that have a Mapping Quality < 10 / TotalReads X X
PairedReads(%) # of reads marked paired in the flag / TotalReads X X
ProperPaired(%) # of reads marked paired AND proper paired in the flag / TotalReads X X
DupRate(%) # of reads marked duplicate in the flag / TotalReads
QCFailRate(%) # of reads marked QC failure in the flag / TotalReads
AverageMapQuality sum of included mapping qualities / AverageMapQualCount X X X
AverageMapQualCount # of mapping qualities in AverageMapQuality X X X

This output does not include a MapQual255 count in version 1.0.

Sample Output
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

Count-Based Output Format

Field Description Excludes Duplicates, QC Failures Excludes Unmapped Excludes MapQual = 255 Excludes Below Min MapQual
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)
TotalReads # of reads that span this position
Dups # of reads marked duplicate in the flag
QCFail # of reads marked QC failure in the flag
Mapped # of reads marked mapped in the flag X X
Paired # of reads marked paired in the flag X X
ProperPaired # of reads marked paired AND proper paired in the flag X X
ZeroMapQual # of reads that have a Mapping Quality of 0 X X
MapQual<10(%) # of reads that have a Mapping Quality < 10 X X
MapQual255 # of reads that have a Mapping Quality = 255 X X
PassMapQual # of reads that have a Mapping Quality >= a minimum Mapping Quality X X
AverageMapQuality sum of included mapping qualities / AverageMapQualCount X X X
AverageMapQualCount # of mapping qualities in AverageMapQuality X X X
Depth # of reads that are mapped with acceptable Mapping Quality, and are not duplicates or QC failures X X X
Q20Bases # of bases at this position with a base quality (from the read) of Q20 or higher X X X