Summary 

Globals

Reference size 3,095,693,983
Number of reads 30,554,870
Mapped reads 26,597,785 / 87.05%
Unmapped reads 3,957,085 / 12.95%
Paired reads 0 / 0%
Read min/max/mean length 100 / 100 / 100
Clipped reads 120 / 0%
Duplication rate 11.47%

ACGT Content

Number/percentage of A's 758,030,990 / 28.5%
Number/percentage of C's 570,698,935 / 21.46%
Number/percentage of T's 759,502,271 / 28.56%
Number/percentage of G's 571,284,184 / 21.48%
Number/percentage of N's 0 / 0%
GC Percentage 42.94%

Coverage

Mean 0.86
Standard Deviation 4.23

Mapping Quality

Mean Mapping Quality 32.26

Indels

Total reads with indels 533,198
Insertions 124,931
Deletions 408,267
Homopolymer indels 69.03%

Chromosome stats

Name Length Mapped bases Mean coverage Standard deviation
chr1 249250621 251715580 1.01 9.11
chr2 243199373 203032624 0.83 1.52
chr3 198022430 160617960 0.81 1.83
chr4 191154276 153785593 0.8 1.53
chr5 180915260 148913667 0.82 1.15
chr6 171115067 153703941 0.9 2.49
chr7 159138663 136902887 0.86 9.66
chr8 146364022 129519534 0.88 1.79
chr9 141213431 104201074 0.74 0.67
chr10 135534747 116971775 0.86 8.85
chr11 135006516 117843387 0.87 1.11
chr12 133851895 114360048 0.85 1.13
chr13 115169878 88451861 0.77 0.64
chr14 107349540 113893706 1.06 1.37
chr15 102531392 74019314 0.72 0.69
chr16 90354753 82393440 0.91 4.02
chr17 81195210 78417060 0.97 1.03
chr18 78077248 43613454 0.56 1.92
chr19 59128983 83955303 1.42 2.45
chr20 63025520 87382338 1.39 1.44
chr21 48129895 36029747 0.75 2.11
chr22 51304566 35442699 0.69 0.72
chrX 155270560 138893607 0.89 2.05
chrY 59373566 5452683 0.09
chrM 16571 575263 34.72 9.79

Input data and parameters 

Alignment

BAM file: /data/mb169-DNA-damage/mapping/max/18h_3.bwa.bam
Program: bwa (0.6.1-r104)
Size of a homopolymer: 3
Number of windows: 400
Analysis date: Tue Feb 04 20:57:35 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