Input data and parameters 

QualiMap command line

qualimap bamqc -bam /scratch/108818/ANALYSIS/P4107/piper_ngi/05_processed_alignments/P4107_1005.clean.dedup.bam -c -nw 400 -hm 3

Alignment

BAM file: /scratch/108818/ANALYSIS/P4107/piper_ngi/05_processed_alignments/P4107_1005.clean.dedup.bam
Program: bwa (0.7.12-r1039)
Size of a homopolymer: 3
Number of windows: 400
Analysis date: Wed Feb 24 19:27:47 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 41,766,247,932 / 29.56%
Number/percentage of C's 28,830,731,831 / 20.4%
Number/percentage of T's 41,982,783,948 / 29.71%
Number/percentage of G's 28,717,868,388 / 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 50.34

Insert size

Mean 30,723.18
Standard Deviation 1,719,964.24
P25/Median/P75 315 / 365 / 415

Mismatches and indels

General error rate 0.71%
Mismatches 936,352,861
Insertions 19,387,261
Deletions 20,279,198
Homopolymer indels 55.68%

Chromosome stats

Name Length Mapped bases Mean coverage Standard deviation
1 249250621 11570829902 46.42 1,310.87
2 243199373 11944995834 49.12 310.41
3 198022430 9294503678 46.94 29.56
4 191154276 9404231256 49.2 536.6
5 180915260 8478668891 46.87 21.91
6 171115067 8159625548 47.69 269.63
7 159138663 7531940086 47.33 230.26
8 146364022 7422232209 50.71 1,720.78
9 141213431 5835541862 41.32 276.83
10 135534747 7394870863 54.56 1,040.74
11 135006516 6434577165 47.66 239.46
12 133851895 6375574482 47.63 25.49
13 115169878 4518955660 39.24 20.19
14 107349540 4296947409 40.03 26.99
15 102531392 4024842623 39.25 25.64
16 90354753 4304554003 47.64 275.4
17 81195210 3903887396 48.08 163.9
18 78077248 3661451616 46.9 224.58
19 59128983 2834809969 47.94 619.53
20 63025520 2909008343 46.16 132.31
21 48129895 1894311427 39.36 206.11
22 51304566 1714293129 33.41 144.53
X 155270560 3740631522 24.09 65.14
Y 59373566 1500809941 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 3906550 196.18 93.35
GL000231.1 27386 5469774 199.73 114.48
GL000210.1 27682 581830 21.02 8.86
GL000239.1 33824 4260119 125.95 65.16
GL000235.1 34474 6342569 183.98 169.42
GL000201.1 36148 780012 21.58 14.75
GL000247.1 36422 2336109 64.14 34.07
GL000245.1 36651 4566636 124.6 65.25
GL000197.1 37175 838886 22.57 6.32
GL000203.1 37498 2603170 69.42 57.28
GL000246.1 38154 1167721 30.61 11.81
GL000249.1 38502 864946 22.46 5.99
GL000196.1 38914 890141 22.87 6.64
GL000248.1 39786 901794 22.67 10.05
GL000244.1 39929 1663362 41.66 20.18
GL000238.1 39939 1112476 27.85 11.31
GL000202.1 40103 1322427 32.98 13.04
GL000234.1 40531 10092339 249 96.34
GL000232.1 40652 13554702 333.43 125.76
GL000206.1 41001 1104845 26.95 9.84
GL000240.1 41933 3334783 79.53 42.86
GL000236.1 41934 1610672 38.41 18.7
GL000241.1 42152 10991441 260.76 133.21
GL000243.1 43341 4393322 101.37 76.71
GL000242.1 43523 900792 20.7 9.29
GL000230.1 43691 3874000 88.67 32.28
GL000237.1 45867 6659728 145.2 63.89
GL000233.1 45941 4366725 95.05 36.53
GL000204.1 81310 2990175 36.77 15.41
GL000198.1 90085 15576037 172.9 204.41
GL000208.1 92689 23840331 257.21 719.56
GL000191.1 106433 3069220 28.84 12.58
GL000227.1 128374 2990978 23.3 13.95
GL000228.1 129120 45958629 355.94 2,313.88
GL000214.1 137718 33878539 246 198.05
GL000221.1 155397 20630792 132.76 74.59
GL000209.1 159169 3985460 25.04 7.32
GL000218.1 161147 17816064 110.56 39.6
GL000220.1 161802 388542312 2,401.34 3,418.42
GL000213.1 164239 3333121 20.29 9.2
GL000211.1 166566 10036059 60.25 25.67
GL000199.1 169874 402522218 2,369.53 5,789.11
GL000217.1 172149 12935192 75.14 45.77
GL000216.1 172294 106339097 617.2 3,271.89
GL000215.1 172545 3506754 20.32 9.91
GL000205.1 174588 28951158 165.83 90.47
GL000219.1 179198 26035875 145.29 120.68
GL000224.1 179693 45733230 254.51 430.43
GL000223.1 180455 4484144 24.85 7.78
GL000195.1 182896 33880159 185.24 60.06
GL000212.1 186858 85217875 456.06 6,085.35
GL000222.1 186861 13669774 73.15 252.78
GL000200.1 187035 2979179 15.93 7.73
GL000193.1 189789 23360584 123.09 67.37
GL000194.1 191469 23918065 124.92 63.59
GL000225.1 211173 111090613 526.06 1,309.41
GL000192.1 547496 24923127 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