Summary 

Globals

Reference size 3,095,693,983
Number of reads 41,325,641
Mapped reads 36,036,351 / 87.2%
Unmapped reads 5,289,290 / 12.8%
Paired reads 0 / 0%
Read min/max/mean length 100 / 100 / 100
Clipped reads 155 / 0%
Duplication rate 3.47%

ACGT Content

Number/percentage of A's 1,026,958,581 / 28.5%
Number/percentage of C's 773,886,462 / 21.48%
Number/percentage of T's 1,028,652,097 / 28.55%
Number/percentage of G's 773,786,635 / 21.47%
Number/percentage of N's 0 / 0%
GC Percentage 42.95%

Coverage

Mean 1.16
Standard Deviation 6.17

Mapping Quality

Mean Mapping Quality 32.38

Indels

Total reads with indels 661,821
Insertions 165,080
Deletions 496,741
Homopolymer indels 70.63%

Chromosome stats

Name Length Mapped bases Mean coverage Standard deviation
chr1 249250621 346530284 1.39 14.04
chr2 243199373 278591236 1.15 2.17
chr3 198022430 222341262 1.12 2.6
chr4 191154276 202537705 1.06 1.37
chr5 180915260 202370160 1.12 0.87
chr6 171115067 208209595 1.22 3.39
chr7 159138663 185262443 1.16 14.2
chr8 146364022 175739846 1.2 2.36
chr9 141213431 141210167 1 1
chr10 135534747 159940307 1.18 12.47
chr11 135006516 157272638 1.16 1.28
chr12 133851895 156789929 1.17 0.79
chr13 115169878 120932558 1.05 0.95
chr14 107349540 156667434 1.46 1.37
chr15 102531392 101733186 0.99 1.01
chr16 90354753 111044941 1.23 5.52
chr17 81195210 105006785 1.29 1.15
chr18 78077248 57380224 0.73 1.21
chr19 59128983 113252371 1.92 3.05
chr20 63025520 114811596 1.82 1.3
chr21 48129895 44891153 0.93 1.77
chr22 51304566 47237895 0.92 1.07
chrX 155270560 184349486 1.19 2.93
chrY 59373566 4512493 0.08
chrM 16571 5382471 324.81 80.54

Input data and parameters 

Alignment

BAM file: /data/mb169-DNA-damage/mapping/max/NI_3.bwa.bam
Program: bwa (0.6.1-r104)
Size of a homopolymer: 3
Number of windows: 400
Analysis date: Tue Feb 04 18:12:44 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