Input data and parameters 

QualiMap command line

qualimap bamqc -bam /scratch/108823/ANALYSIS/P4107/piper_ngi/05_processed_alignments/P4107_1001.clean.dedup.bam -c -nw 400 -hm 3

Alignment

BAM file: /scratch/108823/ANALYSIS/P4107/piper_ngi/05_processed_alignments/P4107_1001.clean.dedup.bam
Program: bwa (0.7.12-r1039)
Size of a homopolymer: 3
Number of windows: 400
Analysis date: Wed Feb 24 12:24:49 CET 2016
Draw chromosome limits: yes

Summary 

Globals

Reference size 3,101,804,739
Number of reads 772,071,557
Mapped reads 751,147,332 / 97.29%
Unmapped reads 20,924,225 / 2.71%
Paired reads 751,147,332 / 97.29%
Mapped reads, only first in pair 375,903,971 / 48.69%
Mapped reads, only second in pair 375,243,361 / 48.6%
Mapped reads, both in pair 749,705,894 / 97.1%
Mapped reads, singletons 1,441,438 / 0.19%
Read min/max/mean length 30 / 151 / 150.39
Clipped reads 50,331,843 / 6.52%
Duplication rate 16.61%

ACGT Content

Number/percentage of A's 32,672,977,283 / 29.46%
Number/percentage of C's 22,732,803,038 / 20.5%
Number/percentage of T's 32,841,273,469 / 29.61%
Number/percentage of G's 22,647,323,821 / 20.42%
Number/percentage of N's 0 / 0%
GC Percentage 40.92%

Coverage

Mean 35.78
Standard Deviation 491.12

Mapping Quality

Mean Mapping Quality 50.32

Insert size

Mean 28,931.62
Standard Deviation 1,662,618.41
P25/Median/P75 306 / 355 / 406

Mismatches and indels

General error rate 0.8%
Mismatches 836,121,400
Insertions 14,847,635
Deletions 15,566,029
Homopolymer indels 55.48%

Chromosome stats

Name Length Mapped bases Mean coverage Standard deviation
1 249250621 9105489299 36.53 1,068
2 243199373 9356203228 38.47 243.97
3 198022430 7270434410 36.72 22.36
4 191154276 7330875123 38.35 417.4
5 180915260 6626088018 36.63 17.1
6 171115067 6390549766 37.35 217.37
7 159138663 5915360356 37.17 189.38
8 146364022 5786136214 39.53 1,261.57
9 141213431 4582291343 32.45 225.75
10 135534747 5828751978 43.01 840.04
11 135006516 5045932979 37.38 187.55
12 133851895 5004637861 37.39 19.58
13 115169878 3525257414 30.61 15.7
14 107349540 3372543297 31.42 21.18
15 102531392 3171432003 30.93 20.09
16 90354753 3408247021 37.72 215.83
17 81195210 3100340070 38.18 132.46
18 78077248 2870795677 36.77 181.19
19 59128983 2271955511 38.42 505.03
20 63025520 2300118661 36.5 103.18
21 48129895 1488010318 30.92 162.56
22 51304566 1367156875 26.65 117.18
X 155270560 2919803745 18.8 51.56
Y 59373566 1167393430 19.66 472.08
MT 16569 267319881 16,133.74 1,077.11
GL000207.1 4262 245550 57.61 62.16
GL000226.1 15008 208799844 13,912.57 11,083.66
GL000229.1 19913 3159152 158.65 79.04
GL000231.1 27386 4327988 158.04 90.97
GL000210.1 27682 443325 16.01 7.04
GL000239.1 33824 3335009 98.6 51.47
GL000235.1 34474 4970708 144.19 145.48
GL000201.1 36148 604223 16.72 9.56
GL000247.1 36422 1806890 49.61 26.44
GL000245.1 36651 3592177 98.01 52.95
GL000197.1 37175 706090 18.99 5.22
GL000203.1 37498 1977250 52.73 43.64
GL000246.1 38154 941279 24.67 9.6
GL000249.1 38502 702256 18.24 5.08
GL000196.1 38914 724072 18.61 5.31
GL000248.1 39786 737561 18.54 8.09
GL000244.1 39929 1329653 33.3 17.02
GL000238.1 39939 836866 20.95 8.19
GL000202.1 40103 1027457 25.62 10.94
GL000234.1 40531 7957956 196.34 75.94
GL000232.1 40652 10564839 259.88 98.62
GL000206.1 41001 897988 21.9 8.87
GL000240.1 41933 2601987 62.05 32.89
GL000236.1 41934 1283507 30.61 14.9
GL000241.1 42152 8544943 202.72 107.75
GL000243.1 43341 3449413 79.59 57.86
GL000242.1 43523 715964 16.45 7.41
GL000230.1 43691 3039321 69.56 24.01
GL000237.1 45867 5240203 114.25 50.83
GL000233.1 45941 3575976 77.84 29.99
GL000204.1 81310 2332875 28.69 11.79
GL000198.1 90085 12126545 134.61 160.15
GL000208.1 92689 18765909 202.46 566.6
GL000191.1 106433 2428145 22.81 9.94
GL000227.1 128374 2343658 18.26 10.99
GL000228.1 129120 38935453 301.54 1,968.31
GL000214.1 137718 26470572 192.21 159.84
GL000221.1 155397 16047366 103.27 58.29
GL000209.1 159169 3117201 19.58 5.86
GL000218.1 161147 13934690 86.47 29.67
GL000220.1 161802 311220342 1,923.46 2,724.93
GL000213.1 164239 2571587 15.66 7.2
GL000211.1 166566 7725792 46.38 18.79
GL000199.1 169874 318433197 1,874.53 4,623.22
GL000217.1 172149 10058658 58.43 34.62
GL000216.1 172294 86085999 499.65 2,629.95
GL000215.1 172545 2711180 15.71 7.61
GL000205.1 174588 23087486 132.24 71.54
GL000219.1 179198 20347063 113.55 95.89
GL000224.1 179693 36547985 203.39 344.46
GL000223.1 180455 3575782 19.82 6.48
GL000195.1 182896 26580346 145.33 47.36
GL000212.1 186858 68692613 367.62 4,950.42
GL000222.1 186861 10997539 58.85 217.34
GL000200.1 187035 2371917 12.68 6.49
GL000193.1 189789 18259299 96.21 53.02
GL000194.1 191469 19046981 99.48 50.29
GL000225.1 211173 93650597 443.48 1,123.8
GL000192.1 547496 19491534 35.6 18.17

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