Input data and parameters 

QualiMap command line

qualimap bamqc -bam /scratch/108825/ANALYSIS/P4107/piper_ngi/05_processed_alignments/P4107_1002.clean.dedup.bam -c -nw 400 -hm 3

Alignment

BAM file: /scratch/108825/ANALYSIS/P4107/piper_ngi/05_processed_alignments/P4107_1002.clean.dedup.bam
Program: bwa (0.7.12-r1039)
Size of a homopolymer: 3
Number of windows: 400
Analysis date: Wed Feb 24 20:34:51 CET 2016
Draw chromosome limits: yes

Summary 

Globals

Reference size 3,101,804,739
Number of reads 865,975,844
Mapped reads 847,067,526 / 97.82%
Unmapped reads 18,908,318 / 2.18%
Paired reads 847,067,526 / 97.82%
Mapped reads, only first in pair 423,736,526 / 48.93%
Mapped reads, only second in pair 423,331,000 / 48.88%
Mapped reads, both in pair 845,777,619 / 97.67%
Mapped reads, singletons 1,289,907 / 0.15%
Read min/max/mean length 30 / 151 / 150.37
Clipped reads 54,256,947 / 6.27%
Duplication rate 20.69%

ACGT Content

Number/percentage of A's 36,926,389,956 / 29.5%
Number/percentage of C's 25,612,881,110 / 20.46%
Number/percentage of T's 37,117,174,029 / 29.65%
Number/percentage of G's 25,511,344,667 / 20.38%
Number/percentage of N's 0 / 0%
GC Percentage 40.84%

Coverage

Mean 40.38
Standard Deviation 546.29

Mapping Quality

Mean Mapping Quality 50.33

Insert size

Mean 29,317.24
Standard Deviation 1,671,889.99
P25/Median/P75 315 / 364 / 415

Mismatches and indels

General error rate 0.8%
Mismatches 942,335,641
Insertions 16,801,076
Deletions 17,642,343
Homopolymer indels 55.45%

Chromosome stats

Name Length Mapped bases Mean coverage Standard deviation
1 249250621 10269443198 41.2 1,174.31
2 243199373 10570478562 43.46 265.51
3 198022430 8221693206 41.52 25.66
4 191154276 8293094776 43.38 461.45
5 180915260 7495344090 41.43 19.12
6 171115067 7217817848 42.18 242.49
7 159138663 6672783877 41.93 207.9
8 146364022 6542083415 44.7 1,435.87
9 141213431 5172037854 36.63 246.08
10 135534747 6560052900 48.4 919.93
11 135006516 5697073771 42.2 209.63
12 133851895 5648263260 42.2 22
13 115169878 3991842459 34.66 17.58
14 107349540 3807015536 35.46 23.71
15 102531392 3573613240 34.85 22.52
16 90354753 3832938953 42.42 240.89
17 81195210 3482933022 42.9 145.45
18 78077248 3242686452 41.53 200.35
19 59128983 2544220814 43.03 556.93
20 63025520 2589166204 41.08 115.83
21 48129895 1677741003 34.86 182.97
22 51304566 1531901554 29.86 130.8
X 155270560 3303838528 21.28 57.12
Y 59373566 1322568205 22.28 524.63
MT 16569 304187388 18,358.83 1,180.84
GL000207.1 4262 283979 66.63 71.19
GL000226.1 15008 232926234 15,520.14 12,334.76
GL000229.1 19913 3482434 174.88 81.7
GL000231.1 27386 4870727 177.85 102.74
GL000210.1 27682 541179 19.55 7.9
GL000239.1 33824 3768749 111.42 61.27
GL000235.1 34474 5633298 163.41 151.72
GL000201.1 36148 671331 18.57 9.22
GL000247.1 36422 2113594 58.03 30.48
GL000245.1 36651 4041816 110.28 58.24
GL000197.1 37175 757229 20.37 5.42
GL000203.1 37498 2267436 60.47 50.06
GL000246.1 38154 1088121 28.52 10.32
GL000249.1 38502 771459 20.04 5.34
GL000196.1 38914 792320 20.36 5.59
GL000248.1 39786 831166 20.89 9.07
GL000244.1 39929 1504255 37.67 19.05
GL000238.1 39939 950204 23.79 9.17
GL000202.1 40103 1205478 30.06 12.47
GL000234.1 40531 8949391 220.8 83.26
GL000232.1 40652 12081272 297.19 112.95
GL000206.1 41001 1005616 24.53 9.08
GL000240.1 41933 2920968 69.66 35.21
GL000236.1 41934 1423051 33.94 16.83
GL000241.1 42152 9607765 227.93 119.29
GL000243.1 43341 3894003 89.85 67.6
GL000242.1 43523 818246 18.8 8.23
GL000230.1 43691 3442633 78.8 27.36
GL000237.1 45867 5948138 129.68 57.84
GL000233.1 45941 4043095 88.01 33.72
GL000204.1 81310 2651959 32.62 13.79
GL000198.1 90085 13644997 151.47 179.87
GL000208.1 92689 20963070 226.17 629.63
GL000191.1 106433 2787771 26.19 11.55
GL000227.1 128374 2576906 20.07 11.99
GL000228.1 129120 42743535 331.04 2,166.28
GL000214.1 137718 29964137 217.58 179.42
GL000221.1 155397 18102286 116.49 65.62
GL000209.1 159169 3499512 21.99 5.95
GL000218.1 161147 15644082 97.08 33.65
GL000220.1 161802 348438120 2,153.48 3,074.74
GL000213.1 164239 2901358 17.67 7.95
GL000211.1 166566 8929603 53.61 21.02
GL000199.1 169874 355809364 2,094.55 5,096.6
GL000217.1 172149 11377490 66.09 39.28
GL000216.1 172294 95536804 554.5 2,909.24
GL000215.1 172545 3100149 17.97 8.6
GL000205.1 174588 25705377 147.23 80.44
GL000219.1 179198 22887225 127.72 107.49
GL000224.1 179693 40876537 227.48 387.75
GL000223.1 180455 4026314 22.31 7.18
GL000195.1 182896 30188853 165.06 54.99
GL000212.1 186858 76900219 411.54 5,488.89
GL000222.1 186861 12270475 65.67 240.25
GL000200.1 187035 2672004 14.29 7.05
GL000193.1 189789 20614246 108.62 59.3
GL000194.1 191469 21173157 110.58 55.41
GL000225.1 211173 102288696 484.38 1,212.49
GL000192.1 547496 22016567 40.21 20.58

Coverage across reference 

Coverage Histogram 

Coverage Histogram (0-50X) 

Genome Fraction Coverage 

Duplication Rate Histogram 

Mapped Reads Nucleotide Content 

Mapped Reads GC-content Distribution 

Mapped Reads Clipping Profile 

Homopolymer Indels 

Mapping Quality Across Reference 

Mapping Quality Histogram 

Insert Size Across Reference 

Insert Size Histogram