Summary 

Globals

Reference size 3,095,693,983
Number of reads 41,799,267
Mapped reads 38,063,509 / 91.06%
Unmapped reads 3,735,758 / 8.94%
Paired reads 0 / 0%
Read min/max/mean length 94 / 94 / 94
Clipped reads 209 / 0%
Duplication rate 51.55%

ACGT Content

Number/percentage of A's 924,307,470 / 25.83%
Number/percentage of C's 863,688,365 / 24.14%
Number/percentage of T's 926,022,467 / 25.88%
Number/percentage of G's 863,759,500 / 24.14%
Number/percentage of N's 0 / 0%
GC Percentage 48.28%

Coverage

Mean 1.16
Standard Deviation 4.01

Mapping Quality

Mean Mapping Quality 32.23

Indels

Total reads with indels 641,104
Insertions 153,820
Deletions 487,284
Homopolymer indels 69.5%

Chromosome stats

Name Length Mapped bases Mean coverage Standard deviation
chr1 249250621 354929502 1.42 8.18
chr2 243199373 262003350 1.08 2.2
chr3 198022430 195800733 0.99 1.74
chr4 191154276 161419218 0.84 2.3
chr5 180915260 180180062 1 2
chr6 171115067 189624411 1.11 3.13
chr7 159138663 181040541 1.14 9.47
chr8 146364022 154927023 1.06 2.42
chr9 141213431 142710585 1.01 1.99
chr10 135534747 162152654 1.2 3.09
chr11 135006516 160703137 1.19 2.14
chr12 133851895 153585045 1.15 2.16
chr13 115169878 98557469 0.86 1.81
chr14 107349540 153431655 1.43 2.44
chr15 102531392 108492427 1.06 1.97
chr16 90354753 133845407 1.48 2.61
chr17 81195210 139364443 1.72 2.66
chr18 78077248 55733018 0.71 3.08
chr19 59128983 167919167 2.84 3.86
chr20 63025520 137437759 2.18 2.87
chr21 48129895 45590817 0.95 3.48
chr22 51304566 69083949 1.35 2.28
chrX 155270560 160623421 1.03 3.45
chrY 59373566 7084700 0.12 0.99
chrM 16571 2099153 126.68 52.61

Input data and parameters 

Alignment

BAM file: /data/mb169-DNA-damage/mapping/6h_2.bwa.bam
Program: bwa (0.6.1-r104)
Size of a homopolymer: 3
Number of windows: 400
Analysis date: Thu Aug 29 00:42:59 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