BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR3472584.sorted.bam
outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 7,520,116
number of mapped reads = 6,913,710 (91.94%)
number of supplementary alignments = 223,353 (2.97%)
number of secondary alignments = 0
number of mapped paired reads (first in pair) = 3,485,749
number of mapped paired reads (second in pair) = 3,427,961
number of mapped paired reads (both in pair) = 6,750,498
number of mapped paired reads (singletons) = 163,212
number of mapped bases = 562,508,109 bp
number of sequenced bases = 562,267,161 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 974,407
duplication rate = 12.24%
>>>>>>> Insert size
mean insert size = 259,269.9274
std insert size = 4,942,547.8834
median insert size = 131
>>>>>>> Mapping quality
mean mapping quality = 50.4283
>>>>>>> ACTG content
number of A's = 144,380,401 bp (25.68%)
number of C's = 112,357,877 bp (19.98%)
number of T's = 167,538,047 bp (29.8%)
number of G's = 137,615,567 bp (24.48%)
number of N's = 375,269 bp (0.07%)
GC percentage = 44.46%
>>>>>>> Mismatches and indels
general error rate = 0.0122
number of mismatches = 6,751,373
number of insertions = 55,233
mapped reads with insertion percentage = 0.78%
number of deletions = 128,392
mapped reads with deletion percentage = 1.82%
homopolymer indels = 42.65%
>>>>>>> Coverage
mean coverageData = 0.1817X
std coverageData = 1.6908X
There is a 10.62% of reference with a coverageData >= 1X
There is a 4.44% of reference with a coverageData >= 2X
There is a 1.39% of reference with a coverageData >= 3X
There is a 0.62% of reference with a coverageData >= 4X
There is a 0.27% of reference with a coverageData >= 5X
There is a 0.14% of reference with a coverageData >= 6X
There is a 0.07% of reference with a coverageData >= 7X
There is a 0.04% of reference with a coverageData >= 8X
There is a 0.03% of reference with a coverageData >= 9X
There is a 0.02% of reference with a coverageData >= 10X
There is a 0.02% of reference with a coverageData >= 11X
There is a 0.01% of reference with a coverageData >= 12X
There is a 0.01% of reference with a coverageData >= 13X
There is a 0.01% of reference with a coverageData >= 14X
There is a 0.01% of reference with a coverageData >= 15X
There is a 0.01% of reference with a coverageData >= 16X
There is a 0.01% of reference with a coverageData >= 17X
There is a 0.01% of reference with a coverageData >= 18X
There is a 0.01% of reference with a coverageData >= 19X
There is a 0.01% of reference with a coverageData >= 20X
There is a 0.01% of reference with a coverageData >= 21X
There is a 0.01% of reference with a coverageData >= 22X
There is a 0.01% of reference with a coverageData >= 23X
There is a 0% of reference with a coverageData >= 24X
There is a 0% of reference with a coverageData >= 25X
There is a 0% of reference with a coverageData >= 26X
There is a 0% of reference with a coverageData >= 27X
There is a 0% of reference with a coverageData >= 28X
There is a 0% of reference with a coverageData >= 29X
There is a 0% of reference with a coverageData >= 30X
There is a 0% of reference with a coverageData >= 31X
There is a 0% of reference with a coverageData >= 32X
There is a 0% of reference with a coverageData >= 33X
There is a 0% of reference with a coverageData >= 34X
There is a 0% of reference with a coverageData >= 35X
There is a 0% of reference with a coverageData >= 36X
There is a 0% of reference with a coverageData >= 37X
There is a 0% of reference with a coverageData >= 38X
There is a 0% of reference with a coverageData >= 39X
There is a 0% of reference with a coverageData >= 40X
There is a 0% of reference with a coverageData >= 41X
There is a 0% of reference with a coverageData >= 42X
There is a 0% of reference with a coverageData >= 43X
There is a 0% of reference with a coverageData >= 44X
There is a 0% of reference with a coverageData >= 45X
There is a 0% of reference with a coverageData >= 46X
There is a 0% of reference with a coverageData >= 47X
There is a 0% of reference with a coverageData >= 48X
There is a 0% of reference with a coverageData >= 49X
There is a 0% of reference with a coverageData >= 50X
There is a 0% of reference with a coverageData >= 51X
>>>>>>> Coverage per contig
chr1 249250621 37760370 0.15149559045632227 2.028137047928098
chr2 243199373 57879018 0.23798999679164468 2.5302951042610005
chr3 198022430 30286947 0.15294705251319257 0.5620599667819567
chr4 191154276 28911101 0.15124485627514814 0.9844626923075
chr5 180915260 27231753 0.15052214500866318 0.5944797717436676
chr6 171115067 38419882 0.22452658712981716 1.04681141814486
chr7 159138663 42357496 0.2661672229833928 3.267938707046333
chr8 146364022 28125584 0.1921618688505294 1.4446537753071222
chr9 141213431 19927200 0.14111405592857523 1.8662183914589423
chr10 135534747 22502591 0.16602820677416397 1.439271570016529
chr11 135006516 20941175 0.15511232805978045 1.357678221421617
chr12 133851895 20927858 0.15635085330693302 0.5869331131527109
chr13 115169878 27096645 0.2352754511036297 0.7388641807689649
chr14 107349540 14474910 0.13483905007883593 3.249129155388675
chr15 102531392 13706064 0.1336767572608397 0.5325899822628378
chr16 90354753 21321946 0.23598034737585968 1.0173899519201404
chr17 81195210 22597656 0.27831267386339664 1.6490782429507203
chr18 78077248 12758255 0.1634055416502385 3.089110956202808
chr19 59128983 12770062 0.21596958635327787 1.4553520924795929
chr20 63025520 20172353 0.3200664270600227 1.0723062160412196
chr21 48129895 8796141 0.1827583667074279 0.8245331988533348
chr22 51304566 5969731 0.11635866873915277 0.502756256726041
chrMT 16571 421210 25.41850220264317 15.796643686407638
chrX 155270560 25908002 0.1668571427835386 0.85482909593208
chrY 59373566 1244159 0.020954762932716555 0.7316923523297503