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 |