Summary 

Globals

Reference size 3,095,693,983
Number of reads 34,465,859
Mapped reads 31,250,375 / 90.67%
Unmapped reads 3,215,484 / 9.33%
Paired reads 0 / 0%
Read min/max/mean length 90 / 90 / 90
Clipped reads 131 / 0%
Duplication rate 8.64%

ACGT Content

Number/percentage of A's 828,060,825 / 29.44%
Number/percentage of C's 577,283,114 / 20.53%
Number/percentage of T's 829,166,676 / 29.48%
Number/percentage of G's 577,876,415 / 20.55%
Number/percentage of N's 0 / 0%
GC Percentage 41.07%

Coverage

Mean 0.91
Standard Deviation 5.54

Mapping Quality

Mean Mapping Quality 32.35

Indels

Total reads with indels 451,664
Insertions 125,774
Deletions 325,890
Homopolymer indels 74.78%

Chromosome stats

Name Length Mapped bases Mean coverage Standard deviation
chr1 249250621 267371851 1.07 10.81
chr2 243199373 224156777 0.92 1.77
chr3 198022430 178658844 0.9 3.19
chr4 191154276 170902948 0.89 1.1
chr5 180915260 163975978 0.91 1.09
chr6 171115067 169039790 0.99 2.83
chr7 159138663 145919945 0.92 11.41
chr8 146364022 131182763 0.9 1.79
chr9 141213431 110232206 0.78 0.63
chr10 135534747 129768841 0.96 15.56
chr11 135006516 121280238 0.9 1.09
chr12 133851895 119699886 0.89 0.45
chr13 115169878 114679968 1 1
chr14 107349540 118134787 1.1 0.89
chr15 102531392 75443662 0.74 0.68
chr16 90354753 81621445 0.9 5.93
chr17 81195210 74284002 0.91 1.08
chr18 78077248 43724259 0.56 1.3
chr19 59128983 74770066 1.26 3.52
chr20 63025520 82373466 1.31 1.14
chr21 48129895 32639187 0.68 1.24
chr22 51304566 31764830 0.62 0.79
chrX 155270560 145717188 0.94 2.26
chrY 59373566 3318989 0.06
chrM 16571 2092795 126.29 35

Input data and parameters 

Alignment

BAM file: /data/mb169-DNA-damage/mapping/IR.bwa.bam
Program: bwa (0.6.1-r104)
Size of a homopolymer: 3
Number of windows: 400
Analysis date: Mon May 13 19:26:55 CEST 2013
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