Input data and parameters 

QualiMap command line

qualimap bamqc -bam /scratch/108818/ANALYSIS/P4107/piper_ngi/01_raw_alignments/P4107_1005.AHJHNYCCXX.P4107_1005.6.bam -c -nw 400 -hm 3

Alignment

BAM file: /scratch/108818/ANALYSIS/P4107/piper_ngi/01_raw_alignments/P4107_1005.AHJHNYCCXX.P4107_1005.6.bam
Program: bwa (0.7.12-r1039)
Size of a homopolymer: 3
Number of windows: 400
Analysis date: Sun Feb 21 05:37:02 CET 2016
Draw chromosome limits: yes

Summary 

Globals

Reference size 3,101,804,739
Number of reads 974,955,793
Mapped reads 955,921,317 / 98.05%
Unmapped reads 19,034,476 / 1.95%
Paired reads 955,921,317 / 98.05%
Mapped reads, only first in pair 478,075,695 / 49.04%
Mapped reads, only second in pair 477,845,622 / 49.01%
Mapped reads, both in pair 954,623,839 / 97.91%
Mapped reads, singletons 1,297,478 / 0.13%
Read min/max/mean length 30 / 151 / 150.36
Clipped reads 60,784,864 / 6.23%
Duplication rate 33.48%

ACGT Content

Number/percentage of A's 41,767,109,539 / 29.56%
Number/percentage of C's 28,831,158,534 / 20.4%
Number/percentage of T's 41,983,686,081 / 29.71%
Number/percentage of G's 28,718,309,944 / 20.32%
Number/percentage of N's 0 / 0%
GC Percentage 40.73%

Coverage

Mean 45.58
Standard Deviation 628.1

Mapping Quality

Mean Mapping Quality 50.33

Insert size

Mean 30,722.59
Standard Deviation 1,719,947.74
P25/Median/P75 315 / 365 / 415

Mismatches and indels

General error rate 0.71%
Mismatches 939,525,870
Insertions 18,953,917
Deletions 19,995,628
Homopolymer indels 55.8%

Chromosome stats

Name Length Mapped bases Mean coverage Standard deviation
1 249250621 11570846102 46.42 1,310.87
2 243199373 11945023917 49.12 310.41
3 198022430 9294536815 46.94 29.56
4 191154276 9404218513 49.2 536.6
5 180915260 8478661248 46.87 21.92
6 171115067 8159633505 47.69 269.63
7 159138663 7531944939 47.33 230.26
8 146364022 7422256648 50.71 1,720.78
9 141213431 5835553860 41.32 276.83
10 135534747 7394891525 54.56 1,040.74
11 135006516 6434583127 47.66 239.47
12 133851895 6375604732 47.63 25.49
13 115169878 4518968827 39.24 20.19
14 107349540 4296948124 40.03 26.99
15 102531392 4024855596 39.25 25.64
16 90354753 4304562379 47.64 275.4
17 81195210 3903904340 48.08 163.9
18 78077248 3661458208 46.9 224.58
19 59128983 2834813679 47.94 619.53
20 63025520 2909016768 46.16 132.31
21 48129895 1894317192 39.36 206.11
22 51304566 1714293194 33.41 144.53
X 155270560 3740627328 24.09 65.14
Y 59373566 1500809219 25.28 607.13
MT 16569 344867651 20,814.03 1,330.54
GL000207.1 4262 320238 75.14 78.69
GL000226.1 15008 261705752 17,437.75 13,926.24
GL000229.1 19913 3906544 196.18 93.35
GL000231.1 27386 5469777 199.73 114.48
GL000210.1 27682 581830 21.02 8.86
GL000239.1 33824 4260120 125.95 65.16
GL000235.1 34474 6342550 183.98 169.42
GL000201.1 36148 780012 21.58 14.75
GL000247.1 36422 2336115 64.14 34.07
GL000245.1 36651 4566643 124.6 65.25
GL000197.1 37175 838886 22.57 6.32
GL000203.1 37498 2602933 69.42 57.28
GL000246.1 38154 1167713 30.61 11.81
GL000249.1 38502 864946 22.46 5.99
GL000196.1 38914 890141 22.87 6.64
GL000248.1 39786 901792 22.67 10.05
GL000244.1 39929 1663361 41.66 20.18
GL000238.1 39939 1112488 27.85 11.31
GL000202.1 40103 1322044 32.97 13.06
GL000234.1 40531 10091977 248.99 96.35
GL000232.1 40652 13555196 333.44 125.76
GL000206.1 41001 1104869 26.95 9.85
GL000240.1 41933 3334779 79.53 42.86
GL000236.1 41934 1610703 38.41 18.7
GL000241.1 42152 10991544 260.76 133.21
GL000243.1 43341 4393279 101.37 76.71
GL000242.1 43523 900784 20.7 9.29
GL000230.1 43691 3873314 88.65 32.31
GL000237.1 45867 6660061 145.2 63.9
GL000233.1 45941 4366636 95.05 36.54
GL000204.1 81310 2990242 36.78 15.42
GL000198.1 90085 15576171 172.91 204.41
GL000208.1 92689 23840306 257.21 719.56
GL000191.1 106433 3069221 28.84 12.58
GL000227.1 128374 2990986 23.3 13.95
GL000228.1 129120 45958625 355.94 2,313.88
GL000214.1 137718 33878702 246 198.05
GL000221.1 155397 20630676 132.76 74.59
GL000209.1 159169 3985478 25.04 7.32
GL000218.1 161147 17816005 110.56 39.6
GL000220.1 161802 388541007 2,401.34 3,418.45
GL000213.1 164239 3332907 20.29 9.2
GL000211.1 166566 10036254 60.25 25.67
GL000199.1 169874 402521448 2,369.53 5,789.12
GL000217.1 172149 12934353 75.13 45.77
GL000216.1 172294 106338989 617.19 3,271.89
GL000215.1 172545 3506758 20.32 9.91
GL000205.1 174588 28949212 165.81 90.49
GL000219.1 179198 26035856 145.29 120.68
GL000224.1 179693 45735706 254.52 430.45
GL000223.1 180455 4484142 24.85 7.78
GL000195.1 182896 33880126 185.24 60.06
GL000212.1 186858 85217997 456.06 6,085.35
GL000222.1 186861 13669743 73.15 252.78
GL000200.1 187035 2979179 15.93 7.73
GL000193.1 189789 23360971 123.09 67.37
GL000194.1 191469 23917969 124.92 63.59
GL000225.1 211173 111090526 526.06 1,309.41
GL000192.1 547496 24923052 45.52 23.74

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