Summary 

Globals

Reference size 63,025,520
Number of reads 2,939,810
Mapped reads 2,914,581 / 99.14%
Unmapped reads 25,229 / 0.86%
Paired reads 2,904,345 / 98.79%
Mapped reads, only first in pair 1,453,937 / 49.46%
Mapped reads, only second in pair 1,450,408 / 49.34%
Mapped reads, both in pair 2,896,042 / 98.51%
Mapped reads, singletons 8,303 / 0.28%
Read min/max/mean length 100 / 100 / 100
Clipped reads 678,220 / 23.07%
Duplication rate 3.94%

ACGT Content

Number/percentage of A's 78,482,215 / 28.24%
Number/percentage of C's 59,888,941 / 21.55%
Number/percentage of T's 79,422,510 / 28.58%
Number/percentage of G's 60,086,521 / 21.62%
Number/percentage of N's 0 / 0%
GC Percentage 43.18%

Coverage

Mean 4.41
Standard Deviation 2.75

Mapping Quality

Mean Mapping Quality 55.36

Indels

Total reads with indels 49,586
Insertions 22,503
Deletions 27,083
Homopolymer indels 38.23%

Insert size

Mean 175.02
Median 184

Per chromosome statistics

Name Length Mapped bases Mean coverage Standard deviation
20 63025520 277880187 4.41 2.75

Input data and parameters 

Alignment

BAM file: /home/kokonech/sample_data/HG00096.chrom20.ILLUMINA.bwa.GBR.low_coverage.20101123.reheadered.bam
Program: GATK IndelRealigner (1.0.4487)
Command line: SNPsFileForDebugging=null targetIntervals=/lustre/scratch105/projects/g1k/ref/broad_recal_data/pilot_data/indel.dbsnp_129_b37-vs-pilot.intervals output=null useOnlyKnownIndels=true maxReadsForConsensuses=120 maxConsensuses=30 entropyThreshold=0.15 indelsFileForDebugging=null noOriginalAlignmentTags=false realignReadsWithBadMates=false maxReadsForRealignment=20000 noPGTag=false LODThresholdForCleaning=0.4 maxReadsInRam=500000 targetIntervalsAreNotSorted=false sortInCoordinateOrderEvenThoughItIsHighlyUnsafe=false statisticsFileForDebugging=null
Number of windows: 400
Analysis date: Mon Jul 23 17:04:24 CEST 2012
Draw chromosome limits: yes

Coverage across reference 

Coverage Histogram 

Coverage Histogram (0-50X) 

Duplication Rate Histogram 

Genome Fraction Coverage 

Mapped Reads Nucleotide Content 

Mapped Reads Clipping Profile 

Mapped Reads GC-content Distribution 

Homopolymer Indels 

Mapping Quality Across Reference 

Mapping Quality Histogram 

Insert Size Across Reference 

Insert Size Histogram