Summary 

Globals

Reference size 3,095,693,983
Number of reads 46,427,947
Mapped reads 42,327,610 / 91.17%
Unmapped reads 4,100,337 / 8.83%
Paired reads 0 / 0%
Read min/max/mean length 94 / 94 / 94
Clipped reads 209 / 0%
Duplication rate 29%

ACGT Content

Number/percentage of A's 1,009,859,218 / 25.38%
Number/percentage of C's 978,247,386 / 24.59%
Number/percentage of T's 1,011,943,039 / 25.43%
Number/percentage of G's 978,532,820 / 24.6%
Number/percentage of N's 0 / 0%
GC Percentage 49.18%

Coverage

Mean 1.29
Standard Deviation 3.78

Mapping Quality

Mean Mapping Quality 32.26

Indels

Total reads with indels 690,558
Insertions 170,299
Deletions 520,259
Homopolymer indels 69.69%

Chromosome stats

Name Length Mapped bases Mean coverage Standard deviation
chr1 249250621 393392446 1.58 6.89
chr2 243199373 287610330 1.18 2.15
chr3 198022430 210402452 1.06 1.69
chr4 191154276 181005597 0.95 3.48
chr5 180915260 198957427 1.1 1.95
chr6 171115067 210305214 1.23 3.08
chr7 159138663 201867886 1.27 8.15
chr8 146364022 170750254 1.17 2.15
chr9 141213431 158646268 1.12 1.93
chr10 135534747 179656606 1.33 2.69
chr11 135006516 181593775 1.35 2.28
chr12 133851895 171156378 1.28 2.32
chr13 115169878 105290436 0.91 1.78
chr14 107349540 168220466 1.57 2.56
chr15 102531392 118640142 1.16 1.91
chr16 90354753 150615290 1.67 2.69
chr17 81195210 163195810 2.01 2.82
chr18 78077248 62286034 0.8 4.51
chr19 59128983 189384063 3.2 3.84
chr20 63025520 157581813 2.5 3.28
chr21 48129895 53823635 1.12 5.27
chr22 51304566 79343821 1.55 2.37
chrX 155270560 173684265 1.12 3.43
chrY 59373566 10421518 0.18 1.72
chrM 16571 1351962 81.59 39.07

Input data and parameters 

Alignment

BAM file: /data/mb169-DNA-damage/mapping/18h_2.bwa.bam
Program: bwa (0.6.1-r104)
Size of a homopolymer: 3
Number of windows: 400
Analysis date: Thu Aug 29 03:40:36 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