Summary 

Globals

Reference size 3,095,693,983
Number of reads 34,969,510
Mapped reads 30,835,875 / 88.18%
Unmapped reads 4,133,635 / 11.82%
Paired reads 0 / 0%
Read min/max/mean length 100 / 100 / 100
Clipped reads 132 / 0%
Duplication rate 5.08%

ACGT Content

Number/percentage of A's 881,738,902 / 28.6%
Number/percentage of C's 658,751,935 / 21.37%
Number/percentage of T's 883,418,349 / 28.65%
Number/percentage of G's 659,374,057 / 21.39%
Number/percentage of N's 0 / 0%
GC Percentage 42.75%

Coverage

Mean 1
Standard Deviation 4.67

Mapping Quality

Mean Mapping Quality 32.52

Indels

Total reads with indels 597,463
Insertions 143,987
Deletions 453,476
Homopolymer indels 70.32%

Chromosome stats

Name Length Mapped bases Mean coverage Standard deviation
chr1 249250621 296728865 1.19 9.36
chr2 243199373 238814514 0.98 1.43
chr3 198022430 189590021 0.96 2.02
chr4 191154276 172849040 0.9 1.09
chr5 180915260 172660487 0.95 1.04
chr6 171115067 177566767 1.04 2.81
chr7 159138663 157717428 0.99 11.53
chr8 146364022 150490153 1.03 1.72
chr9 141213431 121182874 0.86 0.51
chr10 135534747 136951744 1.01 10.53
chr11 135006516 134331123 0.99 1
chr12 133851895 131964484 0.99 1.01
chr13 115169878 103204319 0.9 1.09
chr14 107349540 133588287 1.24 1.2
chr15 102531392 86886505 0.85 0.53
chr16 90354753 96529923 1.07 4.78
chr17 81195210 89942272 1.11 1.33
chr18 78077248 47774370 0.61 0.79
chr19 59128983 97667434 1.65 2.3
chr20 63025520 98645675 1.57 1.25
chr21 48129895 37545410 0.78 1.18
chr22 51304566 41192481 0.8 0.6
chrX 155270560 165986672 1.07 2.42
chrY 59373566 3330641 0.06
chrM 16571 784684 47.35 12.99

Input data and parameters 

Alignment

BAM file: /data/mb169-DNA-damage/mapping/max/IR_3.bwa.bam
Program: bwa (0.6.1-r104)
Size of a homopolymer: 3
Number of windows: 400
Analysis date: Tue Feb 25 12:27:20 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