BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR504616.sorted.bam
outfile = /mainsd2/zhouyj/SRP013572/SRP013572.result/quality.files/genome_results.txt
>>>>>>> Reference
number of bases = 3,095,693,983 bp
number of contigs = 25
>>>>>>> Globals
number of windows = 424
number of reads = 302,021,688
number of mapped reads = 286,786,320 (94.96%)
number of supplementary alignments = 3,116,350 (1.03%)
number of secondary alignments = 0
number of mapped paired reads (first in pair) = 143,826,132
number of mapped paired reads (second in pair) = 142,960,188
number of mapped paired reads (both in pair) = 282,619,542
number of mapped paired reads (singletons) = 4,166,778
number of mapped bases = 27,648,268,973 bp
number of sequenced bases = 27,622,325,158 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 85,651,415
duplication rate = 18.41%
>>>>>>> Insert size
mean insert size = 115,172.7817
std insert size = 3,199,095.9591
median insert size = 336
>>>>>>> Mapping quality
mean mapping quality = 52.353
>>>>>>> ACTG content
number of A's = 7,363,065,259 bp (26.66%)
number of C's = 6,402,831,587 bp (23.18%)
number of T's = 7,441,309,049 bp (26.94%)
number of G's = 6,410,044,789 bp (23.21%)
number of N's = 5,074,474 bp (0.02%)
GC percentage = 46.39%
>>>>>>> Mismatches and indels
general error rate = 0.0112
number of mismatches = 275,884,282
number of insertions = 8,448,096
mapped reads with insertion percentage = 2.72%
number of deletions = 7,872,225
mapped reads with deletion percentage = 2.56%
homopolymer indels = 34.57%
>>>>>>> Coverage
mean coverageData = 8.9312X
std coverageData = 220.795X
There is a 83.16% of reference with a coverageData >= 1X
There is a 74.38% of reference with a coverageData >= 2X
There is a 66.06% of reference with a coverageData >= 3X
There is a 58.67% of reference with a coverageData >= 4X
There is a 52.15% of reference with a coverageData >= 5X
There is a 46.43% of reference with a coverageData >= 6X
There is a 41.38% of reference with a coverageData >= 7X
There is a 36.91% of reference with a coverageData >= 8X
There is a 32.94% of reference with a coverageData >= 9X
There is a 29.41% of reference with a coverageData >= 10X
There is a 26.26% of reference with a coverageData >= 11X
There is a 23.44% of reference with a coverageData >= 12X
There is a 20.93% of reference with a coverageData >= 13X
There is a 18.68% of reference with a coverageData >= 14X
There is a 16.67% of reference with a coverageData >= 15X
There is a 14.88% of reference with a coverageData >= 16X
There is a 13.28% of reference with a coverageData >= 17X
There is a 11.85% of reference with a coverageData >= 18X
There is a 10.59% of reference with a coverageData >= 19X
There is a 9.46% of reference with a coverageData >= 20X
There is a 8.46% of reference with a coverageData >= 21X
There is a 7.56% of reference with a coverageData >= 22X
There is a 6.77% of reference with a coverageData >= 23X
There is a 6.07% of reference with a coverageData >= 24X
There is a 5.44% of reference with a coverageData >= 25X
There is a 4.89% of reference with a coverageData >= 26X
There is a 4.4% of reference with a coverageData >= 27X
There is a 3.97% of reference with a coverageData >= 28X
There is a 3.58% of reference with a coverageData >= 29X
There is a 3.24% of reference with a coverageData >= 30X
There is a 2.93% of reference with a coverageData >= 31X
There is a 2.66% of reference with a coverageData >= 32X
There is a 2.42% of reference with a coverageData >= 33X
There is a 2.21% of reference with a coverageData >= 34X
There is a 2.02% of reference with a coverageData >= 35X
There is a 1.85% of reference with a coverageData >= 36X
There is a 1.7% of reference with a coverageData >= 37X
There is a 1.57% of reference with a coverageData >= 38X
There is a 1.45% of reference with a coverageData >= 39X
There is a 1.34% of reference with a coverageData >= 40X
There is a 1.25% of reference with a coverageData >= 41X
There is a 1.16% of reference with a coverageData >= 42X
There is a 1.09% of reference with a coverageData >= 43X
There is a 1.02% of reference with a coverageData >= 44X
There is a 0.95% of reference with a coverageData >= 45X
There is a 0.9% of reference with a coverageData >= 46X
There is a 0.85% of reference with a coverageData >= 47X
There is a 0.8% of reference with a coverageData >= 48X
There is a 0.76% of reference with a coverageData >= 49X
There is a 0.72% of reference with a coverageData >= 50X
There is a 0.68% of reference with a coverageData >= 51X
>>>>>>> Coverage per contig
chr1 249250621 2132736581 8.556594853980323 63.04687475946117
chr2 243199373 2192624441 9.015748741260118 234.71620671477777
chr3 198022430 1466196096 7.404192020065605 19.970010570261834
chr4 191154276 2069473761 10.82619653771177 620.0426797631873
chr5 180915260 1430731892 7.908298570280915 33.28867790332488
chr6 171115067 1177066420 6.878800567573632 30.943845313143235
chr7 159138663 1359359698 8.541982648176452 33.53719809001376
chr8 146364022 1290758561 8.81882407549582 154.24282972600207
chr9 141213431 1009920655 7.151732295209229 66.42856471420139
chr10 135534747 1813162451 13.377842148478722 469.300355212872
chr11 135006516 1185476103 8.78088064282764 27.90912329854959
chr12 133851895 1102887538 8.239610937148107 16.839877784424594
chr13 115169878 611827065 5.3123878884372875 13.615441857219329
chr14 107349540 736248032 6.858418135746087 30.090936937951476
chr15 102531392 807703147 7.877618076227815 14.47837668868341
chr16 90354753 1249423713 13.827979951425466 181.6231285970875
chr17 81195210 958846512 11.809151204855558 65.43383887878404
chr18 78077248 628032331 8.043730370722082 255.37553507867815
chr19 59128983 938263828 15.868086687707786 38.007756198201925
chr20 63025520 710992374 11.28102352824697 146.47268262837937
chr21 48129895 461761628 9.594070961509473 196.19350820881183
chr22 51304566 517658550 10.089911880357784 29.536495069465555
chrMT 16571 10691020 645.1644439080321 283.02446121737245
chrX 155270560 1343970446 8.655668183331084 19.085586656610644
chrY 59373566 442456130 7.452072695111491 524.6490281785743