Summary 

Globals

Reference size 3,095,693,983
Number of reads 34,450,248
Mapped reads 30,439,962 / 88.36%
Unmapped reads 4,010,286 / 11.64%
Paired reads 0 / 0%
Read min/max/mean length 90 / 90 / 90
Clipped reads 118 / 0%
Duplication rate 5.05%

ACGT Content

Number/percentage of A's 791,348,384 / 28.89%
Number/percentage of C's 577,609,550 / 21.09%
Number/percentage of T's 792,520,159 / 28.93%
Number/percentage of G's 577,934,294 / 21.1%
Number/percentage of N's 0 / 0%
GC Percentage 42.18%

Coverage

Mean 0.89
Standard Deviation 5.51

Mapping Quality

Mean Mapping Quality 32.26

Indels

Total reads with indels 416,808
Insertions 115,597
Deletions 301,211
Homopolymer indels 73.66%

Chromosome stats

Name Length Mapped bases Mean coverage Standard deviation
chr1 249250621 262830617 1.05 13.22
chr2 243199373 212363110 0.87 1.8
chr3 198022430 168581944 0.85 2.7
chr4 191154276 159530904 0.83 1.14
chr5 180915260 155067121 0.86 1.12
chr6 171115067 160253260 0.94 2.67
chr7 159138663 141075087 0.89 10.31
chr8 146364022 136347002 0.93 1.77
chr9 141213431 107404773 0.76 0.65
chr10 135534747 122234316 0.9 12.58
chr11 135006516 118771310 0.88 1.11
chr12 133851895 117781020 0.88 1.11
chr13 115169878 87951507 0.76 0.65
chr14 107349540 119487510 1.11 0.87
chr15 102531392 76727666 0.75 0.66
chr16 90354753 82654523 0.91 4.49
chr17 81195210 77889544 0.96 1.04
chr18 78077248 46283429 0.59 2.16
chr19 59128983 84595503 1.43 4.24
chr20 63025520 86356513 1.37 1.06
chr21 48129895 36109540 0.75 1.85
chr22 51304566 35824678 0.7 0.72
chrX 155270560 135367692 0.87 2.29
chrY 59373566 4746091 0.08 1
chrM 16571 3567203 215.27 52.39

Input data and parameters 

Alignment

BAM file: /data/mb169-DNA-damage/mapping/6h.bwa.bam
Program: bwa (0.6.1-r104)
Size of a homopolymer: 3
Number of windows: 400
Analysis date: Fri Sep 06 12:06:47 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