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 |