Summary 

Globals

Reference size 3,095,693,983
Number of reads 47,999,991
Mapped reads 44,607,607 / 92.93%
Unmapped reads 3,392,384 / 7.07%
Paired reads 0 / 0%
Read min/max/mean length 94 / 94 / 94
Clipped reads 311 / 0%
Duplication rate 43.63%

ACGT Content

Number/percentage of A's 1,089,966,145 / 26%
Number/percentage of C's 1,005,276,444 / 23.98%
Number/percentage of T's 1,091,710,214 / 26.04%
Number/percentage of G's 1,005,930,204 / 23.99%
Number/percentage of N's 0 / 0%
GC Percentage 47.97%

Coverage

Mean 1.35
Standard Deviation 4.51

Mapping Quality

Mean Mapping Quality 32.5

Indels

Total reads with indels 758,719
Insertions 186,314
Deletions 572,405
Homopolymer indels 70.3%

Chromosome stats

Name Length Mapped bases Mean coverage Standard deviation
chr1 249250621 424270848 1.7 9.01
chr2 243199373 310874220 1.28 2.32
chr3 198022430 233649744 1.18 1.9
chr4 191154276 186964426 0.98 1.74
chr5 180915260 213164419 1.18 1.9
chr6 171115067 223102662 1.3 3.51
chr7 159138663 211586716 1.33 11.67
chr8 146364022 182912911 1.25 2.54
chr9 141213431 167677193 1.19 1.89
chr10 135534747 190536116 1.41 5
chr11 135006516 187896597 1.39 2.25
chr12 133851895 178621512 1.33 2.05
chr13 115169878 111706916 0.97 1.75
chr14 107349540 177962360 1.66 2.5
chr15 102531392 126253161 1.23 1.87
chr16 90354753 157819226 1.75 2.82
chr17 81195210 163730783 2.02 2.63
chr18 78077248 60310026 0.77 2.1
chr19 59128983 194925872 3.3 4.14
chr20 63025520 158316323 2.51 2.95
chr21 48129895 49669624 1.03 2.63
chr22 51304566 81002329 1.58 2.35
chrX 155270560 193556823 1.25 3.8
chrY 59373566 5324583 0.09
chrM 16571 1709378 103.15 40.46

Input data and parameters 

Alignment

BAM file: /data/mb169-DNA-damage/mapping/IR_2.bwa.bam
Program: bwa (0.6.1-r104)
Size of a homopolymer: 3
Number of windows: 400
Analysis date: Thu Aug 29 07:06:36 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