Input data and parameters 

QualiMap command line

qualimap bamqc -bam /scratch/109642/ANALYSIS/P4107/piper_ngi/05_processed_alignments/P4107_1003.clean.dedup.bam -c -nw 400 -hm 3

Alignment

BAM file: /scratch/109642/ANALYSIS/P4107/piper_ngi/05_processed_alignments/P4107_1003.clean.dedup.bam
Program: bwa (0.7.12-r1039)
Size of a homopolymer: 3
Number of windows: 400
Analysis date: Tue Mar 01 10:19:26 CET 2016
Draw chromosome limits: yes

Summary 

Globals

Reference size 3,101,804,739
Number of reads 868,204,107
Mapped reads 847,562,410 / 97.62%
Unmapped reads 20,641,697 / 2.38%
Paired reads 847,562,410 / 97.62%
Mapped reads, only first in pair 423,982,099 / 48.83%
Mapped reads, only second in pair 423,580,311 / 48.79%
Mapped reads, both in pair 846,352,079 / 97.48%
Mapped reads, singletons 1,210,331 / 0.14%
Read min/max/mean length 30 / 151 / 150.4
Clipped reads 51,490,392 / 5.93%
Duplication rate 21.13%

ACGT Content

Number/percentage of A's 36,958,346,777 / 29.47%
Number/percentage of C's 25,705,886,186 / 20.5%
Number/percentage of T's 37,151,016,327 / 29.62%
Number/percentage of G's 25,604,417,664 / 20.41%
Number/percentage of N's 0 / 0%
GC Percentage 40.91%

Coverage

Mean 40.46
Standard Deviation 554.82

Mapping Quality

Mean Mapping Quality 50.34

Insert size

Mean 28,161.14
Standard Deviation 1,641,138.97
P25/Median/P75 313 / 363 / 414

Mismatches and indels

General error rate 0.73%
Mismatches 856,143,900
Insertions 17,015,133
Deletions 17,829,422
Homopolymer indels 55.61%

Chromosome stats

Name Length Mapped bases Mean coverage Standard deviation
1 249250621 10296149154 41.31 1,192.62
2 243199373 10581585290 43.51 270.02
3 198022430 8222682173 41.52 25.49
4 191154276 8303385214 43.44 487.83
5 180915260 7498067853 41.45 19.24
6 171115067 7225503299 42.23 243.31
7 159138663 6687067410 42.02 208.87
8 146364022 6551944076 44.76 1,455.29
9 141213431 5182134474 36.7 252.42
10 135534747 6569839002 48.47 927.35
11 135006516 5708281934 42.28 210.8
12 133851895 5656694209 42.26 21.83
13 115169878 3988376171 34.63 17.6
14 107349540 3815039017 35.54 23.9
15 102531392 3585793106 34.97 22.67
16 90354753 3849071212 42.6 241.46
17 81195210 3507497018 43.2 146.93
18 78077248 3245937065 41.57 203.16
19 59128983 2565950856 43.4 561.07
20 63025520 2602200294 41.29 118.32
21 48129895 1680307000 34.91 187.18
22 51304566 1546282182 30.14 131.98
X 155270560 3305438306 21.29 57.6
Y 59373566 1319045046 22.22 544.33
MT 16569 305153980 18,417.16 1,106.12
GL000207.1 4262 284133 66.67 70.03
GL000226.1 15008 233008657 15,525.63 12,447.76
GL000229.1 19913 3595386 180.55 87.61
GL000231.1 27386 4904244 179.08 101.55
GL000210.1 27682 526078 19 8.07
GL000239.1 33824 3872515 114.49 59.93
GL000235.1 34474 5580192 161.87 156.03
GL000201.1 36148 725876 20.08 12.14
GL000247.1 36422 2030785 55.76 29.25
GL000245.1 36651 4030094 109.96 59.26
GL000197.1 37175 797138 21.44 5.7
GL000203.1 37498 2245393 59.88 48.8
GL000246.1 38154 1069684 28.04 10.96
GL000249.1 38502 765511 19.88 5.18
GL000196.1 38914 818039 21.02 5.95
GL000248.1 39786 813607 20.45 9.39
GL000244.1 39929 1507924 37.77 18.15
GL000238.1 39939 935744 23.43 9.19
GL000202.1 40103 1164425 29.04 11.35
GL000234.1 40531 9071997 223.83 87.85
GL000232.1 40652 12026068 295.83 111.76
GL000206.1 41001 995752 24.29 9.18
GL000240.1 41933 2986515 71.22 37.37
GL000236.1 41934 1463677 34.9 17.93
GL000241.1 42152 9754487 231.41 121.01
GL000243.1 43341 3906811 90.14 67.21
GL000242.1 43523 817682 18.79 8.04
GL000230.1 43691 3501216 80.14 28.28
GL000237.1 45867 5996756 130.74 55.73
GL000233.1 45941 4007099 87.22 33.35
GL000204.1 81310 2722983 33.49 13.5
GL000198.1 90085 13702819 152.11 181.13
GL000208.1 92689 21057633 227.19 637.61
GL000191.1 106433 2716221 25.52 10.9
GL000227.1 128374 2642474 20.58 12.27
GL000228.1 129120 43506128 336.94 2,189.3
GL000214.1 137718 30101872 218.58 179.76
GL000221.1 155397 18311972 117.84 65.82
GL000209.1 159169 3527198 22.16 6.21
GL000218.1 161147 15827102 98.22 33.1
GL000220.1 161802 356762934 2,204.94 3,121.52
GL000213.1 164239 2911630 17.73 7.88
GL000211.1 166566 8844362 53.1 21.09
GL000199.1 169874 356131896 2,096.45 5,158.06
GL000217.1 172149 11378666 66.1 39.08
GL000216.1 172294 95912802 556.68 2,893.7
GL000215.1 172545 3095426 17.94 8.48
GL000205.1 174588 25801946 147.79 80.34
GL000219.1 179198 22803149 127.25 106.91
GL000224.1 179693 41064349 228.53 388.91
GL000223.1 180455 4060922 22.5 7.33
GL000195.1 182896 29798334 162.93 53.07
GL000212.1 186858 77650022 415.56 5,555.53
GL000222.1 186861 12426329 66.5 245.09
GL000200.1 187035 2671959 14.29 7.07
GL000193.1 189789 20725645 109.2 59.33
GL000194.1 191469 21427238 111.91 56.53
GL000225.1 211173 103694159 491.04 1,237.04
GL000192.1 547496 22073575 40.32 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