Summary 

Globals

Reference size 3,095,693,983
Number of reads 29,662,078
Mapped reads 26,028,966 / 87.75%
Unmapped reads 3,633,112 / 12.25%
Paired reads 0 / 0%
Read min/max/mean length 90 / 90 / 90
Clipped reads 98 / 0%
Duplication rate 6.99%

ACGT Content

Number/percentage of A's 671,162,864 / 28.65%
Number/percentage of C's 499,320,121 / 21.32%
Number/percentage of T's 672,190,716 / 28.7%
Number/percentage of G's 499,745,298 / 21.33%
Number/percentage of N's 0 / 0%
GC Percentage 42.65%

Coverage

Mean 0.76
Standard Deviation 4.5

Mapping Quality

Mean Mapping Quality 32.21

Indels

Total reads with indels 321,242
Insertions 91,285
Deletions 229,957
Homopolymer indels 73.48%

Chromosome stats

Name Length Mapped bases Mean coverage Standard deviation
chr1 249250621 226379310 0.91 10.16
chr2 243199373 182726479 0.75 1.56
chr3 198022430 144317023 0.73 2.34
chr4 191154276 136520794 0.71 1.22
chr5 180915260 132922157 0.73 0.68
chr6 171115067 137315855 0.8 2.31
chr7 159138663 121446114 0.76 8.57
chr8 146364022 118014904 0.81 1.53
chr9 141213431 92212577 0.65 0.76
chr10 135534747 104711120 0.77 11.06
chr11 135006516 103426802 0.77 0.64
chr12 133851895 100604329 0.75 0.66
chr13 115169878 73893415 0.64 0.77
chr14 107349540 100317514 0.93 1.06
chr15 102531392 64990048 0.63 0.77
chr16 90354753 71300866 0.79 3.92
chr17 81195210 67798305 0.84 1.14
chr18 78077248 37674687 0.48 1.66
chr19 59128983 71826029 1.21 3.39
chr20 63025520 73892140 1.17 1.27
chr21 48129895 29721101 0.62 1.62
chr22 51304566 30882032 0.6 0.8
chrX 155270560 114097924 0.73 1.86
chrY 59373566 3832416 0.06
chrM 16571 1936190 116.84 31.86

Input data and parameters 

Alignment

BAM file: /data/mb169-DNA-damage/mapping/18h.bwa.bam
Program: bwa (0.6.1-r104)
Size of a homopolymer: 3
Number of windows: 400
Analysis date: Mon May 13 18:07:30 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