Summary 

Globals

Reference size 3,095,693,983
Number of reads 37,456,074
Mapped reads 32,680,690 / 87.25%
Unmapped reads 4,775,384 / 12.75%
Paired reads 0 / 0%
Read min/max/mean length 100 / 100 / 100
Clipped reads 120 / 0%
Duplication rate 2.8%

ACGT Content

Number/percentage of A's 937,767,364 / 28.7%
Number/percentage of C's 695,166,743 / 21.27%
Number/percentage of T's 939,517,357 / 28.75%
Number/percentage of G's 695,298,381 / 21.28%
Number/percentage of N's 0 / 0%
GC Percentage 42.55%

Coverage

Mean 1.06
Standard Deviation 5.25

Mapping Quality

Mean Mapping Quality 32.39

Indels

Total reads with indels 600,292
Insertions 150,206
Deletions 450,086
Homopolymer indels 70.92%

Chromosome stats

Name Length Mapped bases Mean coverage Standard deviation
chr1 249250621 314904156 1.26 11.81
chr2 243199373 253784638 1.04 1.98
chr3 198022430 202790428 1.02 2.23
chr4 191154276 185689268 0.97 1.03
chr5 180915260 184169883 1.02 0.98
chr6 171115067 190137471 1.11 2.96
chr7 159138663 167974785 1.06 12.08
chr8 146364022 160253177 1.09 1.95
chr9 141213431 127897157 0.91 1.09
chr10 135534747 144636249 1.07 10.72
chr11 135006516 142989524 1.06 0.94
chr12 133851895 142547994 1.06 0.93
chr13 115169878 109967396 0.95 1.04
chr14 107349540 141571530 1.32 1.12
chr15 102531392 91994215 0.9 1.09
chr16 90354753 99294935 1.1 4.88
chr17 81195210 94323935 1.16 1.28
chr18 78077248 52078289 0.67 1.25
chr19 59128983 101096121 1.71 2.66
chr20 63025520 103484085 1.64 1.14
chr21 48129895 40289350 0.84 1.52
chr22 51304566 42323225 0.82 0.57
chrX 155270560 166119874 1.07 2.62
chrY 59373566 4186982 0.07
chrM 16571 3893242 234.94 56.21

Input data and parameters 

Alignment

BAM file: /data/mb169-DNA-damage/mapping/max/6h_3.bwa.bam
Program: bwa (0.6.1-r104)
Size of a homopolymer: 3
Number of windows: 400
Analysis date: Tue Feb 04 19:39:19 CET 2014
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