Summary 

Globals

Reference size 3,095,693,983
Number of reads 32,802,597
Mapped reads 26,736,362 / 81.51%
Unmapped reads 6,066,235 / 18.49%
Paired reads 0 / 0%
Read min/max/mean length 90 / 90 / 90
Clipped reads 101 / 0%
Duplication rate 10.69%

ACGT Content

Number/percentage of A's 692,456,852 / 28.78%
Number/percentage of C's 509,883,572 / 21.19%
Number/percentage of T's 693,656,993 / 28.83%
Number/percentage of G's 510,090,697 / 21.2%
Number/percentage of N's 0 / 0%
GC Percentage 42.39%

Coverage

Mean 0.78
Standard Deviation 4.46

Mapping Quality

Mean Mapping Quality 32.01

Indels

Total reads with indels 355,986
Insertions 97,720
Deletions 258,266
Homopolymer indels 73.33%

Chromosome stats

Name Length Mapped bases Mean coverage Standard deviation
chr1 249250621 229140623 0.92 10.64
chr2 243199373 186589893 0.77 1.55
chr3 198022430 147997133 0.75 2.11
chr4 191154276 139509772 0.73 1.57
chr5 180915260 134413345 0.74 0.67
chr6 171115067 140330800 0.82 2.31
chr7 159138663 124582689 0.78 8.45
chr8 146364022 107703484 0.74 1.57
chr9 141213431 95120469 0.67 0.74
chr10 135534747 109159267 0.81 9.76
chr11 135006516 106895680 0.79 1.17
chr12 133851895 103473700 0.77 0.63
chr13 115169878 93549434 0.81 0.58
chr14 107349540 103266086 0.96 1.04
chr15 102531392 66969477 0.65 0.76
chr16 90354753 71710852 0.79 3.66
chr17 81195210 69676106 0.86 1.12
chr18 78077248 39488532 0.51 2.18
chr19 59128983 72535140 1.23 3.39
chr20 63025520 76840915 1.22 1.23
chr21 48129895 31437490 0.65 1.89
chr22 51304566 30969153 0.6 0.8
chrX 155270560 117120953 0.75 1.85
chrY 59373566 4772293 0.08 1
chrM 16571 3195484 192.84 48.43

Input data and parameters 

Alignment

BAM file: /data/mb169-DNA-damage/mapping/NI.bwa.bam
Program: bwa (0.6.1-r104)
Size of a homopolymer: 3
Number of windows: 400
Analysis date: Mon May 13 16:22:45 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