Input data and parameters 

QualiMap command line

qualimap bamqc -bam /scratch/109642/ANALYSIS/P4107/piper_ngi/01_raw_alignments/P4107_1003.AHJHNYCCXX.P4107_1003.4.bam -c -nw 400 -hm 3

Alignment

BAM file: /scratch/109642/ANALYSIS/P4107/piper_ngi/01_raw_alignments/P4107_1003.AHJHNYCCXX.P4107_1003.4.bam
Program: bwa (0.7.12-r1039)
Size of a homopolymer: 3
Number of windows: 400
Analysis date: Sat Feb 27 01:19:00 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 36,959,138,992 / 29.47%
Number/percentage of C's 25,706,286,957 / 20.5%
Number/percentage of T's 37,151,841,815 / 29.62%
Number/percentage of G's 25,604,832,339 / 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 28,160.72
Standard Deviation 1,641,126.83
P25/Median/P75 313 / 363 / 414

Mismatches and indels

General error rate 0.73%
Mismatches 859,043,227
Insertions 16,626,880
Deletions 17,574,018
Homopolymer indels 55.69%

Chromosome stats

Name Length Mapped bases Mean coverage Standard deviation
1 249250621 10296158389 41.31 1,192.62
2 243199373 10581611065 43.51 270.02
3 198022430 8222707901 41.52 25.49
4 191154276 8303390472 43.44 487.83
5 180915260 7498063496 41.45 19.24
6 171115067 7225524490 42.23 243.31
7 159138663 6687083283 42.02 208.87
8 146364022 6551963803 44.76 1,455.29
9 141213431 5182144145 36.7 252.42
10 135534747 6569864928 48.47 927.35
11 135006516 5708287620 42.28 210.8
12 133851895 5656716696 42.26 21.84
13 115169878 3988392865 34.63 17.61
14 107349540 3815044663 35.54 23.9
15 102531392 3585804273 34.97 22.67
16 90354753 3849074472 42.6 241.46
17 81195210 3507505503 43.2 146.93
18 78077248 3245942584 41.57 203.16
19 59128983 2565960079 43.4 561.07
20 63025520 2602208251 41.29 118.32
21 48129895 1680317755 34.91 187.18
22 51304566 1546277720 30.14 131.98
X 155270560 3305436813 21.29 57.6
Y 59373566 1319045024 22.22 544.33
MT 16569 305153980 18,417.16 1,106.12
GL000207.1 4262 284151 66.67 70.04
GL000226.1 15008 233008657 15,525.63 12,447.76
GL000229.1 19913 3595523 180.56 87.61
GL000231.1 27386 4904265 179.08 101.55
GL000210.1 27682 526078 19 8.07
GL000239.1 33824 3872511 114.49 59.93
GL000235.1 34474 5580182 161.87 156.03
GL000201.1 36148 725876 20.08 12.14
GL000247.1 36422 2030810 55.76 29.25
GL000245.1 36651 4030095 109.96 59.26
GL000197.1 37175 797138 21.44 5.7
GL000203.1 37498 2245104 59.87 48.79
GL000246.1 38154 1069656 28.04 10.96
GL000249.1 38502 765511 19.88 5.18
GL000196.1 38914 818039 21.02 5.95
GL000248.1 39786 813613 20.45 9.39
GL000244.1 39929 1507922 37.77 18.15
GL000238.1 39939 935758 23.43 9.19
GL000202.1 40103 1164120 29.03 11.36
GL000234.1 40531 9072001 223.83 87.85
GL000232.1 40652 12026406 295.84 111.76
GL000206.1 41001 995720 24.29 9.18
GL000240.1 41933 2986496 71.22 37.37
GL000236.1 41934 1463749 34.91 17.93
GL000241.1 42152 9754448 231.41 121.01
GL000243.1 43341 3906749 90.14 67.21
GL000242.1 43523 817682 18.79 8.04
GL000230.1 43691 3500616 80.12 28.31
GL000237.1 45867 5996211 130.73 55.76
GL000233.1 45941 4007090 87.22 33.35
GL000204.1 81310 2722991 33.49 13.51
GL000198.1 90085 13702723 152.11 181.13
GL000208.1 92689 21057629 227.19 637.61
GL000191.1 106433 2716246 25.52 10.9
GL000227.1 128374 2642619 20.59 12.28
GL000228.1 129120 43506144 336.94 2,189.3
GL000214.1 137718 30102041 218.58 179.76
GL000221.1 155397 18311988 117.84 65.82
GL000209.1 159169 3527224 22.16 6.21
GL000218.1 161147 15827044 98.21 33.1
GL000220.1 161802 356736142 2,204.77 3,121.64
GL000213.1 164239 2911374 17.73 7.88
GL000211.1 166566 8844470 53.1 21.1
GL000199.1 169874 356131632 2,096.45 5,158.06
GL000217.1 172149 11378394 66.1 39.08
GL000216.1 172294 95913075 556.68 2,893.7
GL000215.1 172545 3095426 17.94 8.48
GL000205.1 174588 25800945 147.78 80.35
GL000219.1 179198 22802293 127.25 106.91
GL000224.1 179693 41063824 228.52 388.91
GL000223.1 180455 4060922 22.5 7.32
GL000195.1 182896 29798311 162.92 53.08
GL000212.1 186858 77650192 415.56 5,555.53
GL000222.1 186861 12426363 66.5 245.09
GL000200.1 187035 2671959 14.29 7.07
GL000193.1 189789 20725708 109.2 59.33
GL000194.1 191469 21427483 111.91 56.53
GL000225.1 211173 103693855 491.04 1,237.04
GL000192.1 547496 22073578 40.32 20.59

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