Summary 

Globals

Reference size 3,095,693,983
Number of reads 44,734,052
Mapped reads 40,854,811 / 91.33%
Unmapped reads 3,879,241 / 8.67%
Paired reads 0 / 0%
Read min/max/mean length 94 / 94 / 94
Clipped reads 255 / 0%
Duplication rate 43.96%

ACGT Content

Number/percentage of A's 988,579,053 / 25.74%
Number/percentage of C's 930,499,372 / 24.23%
Number/percentage of T's 990,366,535 / 25.79%
Number/percentage of G's 930,702,621 / 24.24%
Number/percentage of N's 0 / 0%
GC Percentage 48.47%

Coverage

Mean 1.24
Standard Deviation 4

Mapping Quality

Mean Mapping Quality 32.27

Indels

Total reads with indels 682,503
Insertions 163,252
Deletions 519,251
Homopolymer indels 69.59%

Chromosome stats

Name Length Mapped bases Mean coverage Standard deviation
chr1 249250621 386269401 1.55 8.16
chr2 243199373 280360278 1.15 2.16
chr3 198022430 209013322 1.06 1.7
chr4 191154276 167507714 0.88 2.29
chr5 180915260 190442240 1.05 1.97
chr6 171115067 200894923 1.17 3.1
chr7 159138663 192894026 1.21 9.36
chr8 146364022 162694102 1.11 2.4
chr9 141213431 153115750 1.08 1.96
chr10 135534747 173726127 1.28 3.37
chr11 135006516 173107830 1.28 2.09
chr12 133851895 165346354 1.24 2.12
chr13 115169878 102613662 0.89 1.79
chr14 107349540 166175243 1.55 2.57
chr15 102531392 117881757 1.15 1.92
chr16 90354753 147082090 1.63 2.71
chr17 81195210 156126890 1.92 2.7
chr18 78077248 58385048 0.75 2.91
chr19 59128983 186689428 3.16 4
chr20 63025520 149262343 2.37 2.9
chr21 48129895 49505806 1.03 3.46
chr22 51304566 78052672 1.52 2.38
chrX 155270560 163971659 1.06 3.45
chrY 59373566 6907576 0.12 0.99
chrM 16571 2720905 164.2 68.03

Input data and parameters 

Alignment

BAM file: /data/mb169-DNA-damage/mapping/NI_2.bwa.bam
Program: bwa (0.6.1-r104)
Size of a homopolymer: 3
Number of windows: 400
Analysis date: Wed Aug 28 21:06:08 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