BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR090156.sorted.bam
outfile = /home/luna/rawdata/yangyxdownload/SRP002535/SRP002535.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 = 18,061,838
number of mapped reads = 16,918,088 (93.67%)
number of supplementary alignments = 115,594 (0.64%)
number of secondary alignments = 0
number of mapped bases = 1,103,716,409 bp
number of sequenced bases = 1,103,305,340 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 3,380,214
duplication rate = 13.62%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 46.5441
>>>>>>> ACTG content
number of A's = 287,359,857 bp (26.05%)
number of C's = 198,974,352 bp (18.03%)
number of T's = 352,171,206 bp (31.92%)
number of G's = 264,426,793 bp (23.97%)
number of N's = 373,132 bp (0.03%)
GC percentage = 42%
>>>>>>> Mismatches and indels
general error rate = 0.0059
number of mismatches = 6,347,445
number of insertions = 70,681
mapped reads with insertion percentage = 0.41%
number of deletions = 234,707
mapped reads with deletion percentage = 1.37%
homopolymer indels = 48.38%
>>>>>>> Coverage
mean coverageData = 0.3565X
std coverageData = 2.5292X
There is a 16.28% of reference with a coverageData >= 1X
There is a 8.03% of reference with a coverageData >= 2X
There is a 4.32% of reference with a coverageData >= 3X
There is a 2.43% of reference with a coverageData >= 4X
There is a 1.42% of reference with a coverageData >= 5X
There is a 0.86% of reference with a coverageData >= 6X
There is a 0.54% of reference with a coverageData >= 7X
There is a 0.35% of reference with a coverageData >= 8X
There is a 0.23% of reference with a coverageData >= 9X
There is a 0.16% of reference with a coverageData >= 10X
There is a 0.11% of reference with a coverageData >= 11X
There is a 0.08% of reference with a coverageData >= 12X
There is a 0.06% of reference with a coverageData >= 13X
There is a 0.05% of reference with a coverageData >= 14X
There is a 0.04% of reference with a coverageData >= 15X
There is a 0.03% of reference with a coverageData >= 16X
There is a 0.02% of reference with a coverageData >= 17X
There is a 0.02% of reference with a coverageData >= 18X
There is a 0.02% 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 0.01% of reference with a coverageData >= 24X
There is a 0.01% of reference with a coverageData >= 25X
There is a 0.01% of reference with a coverageData >= 26X
There is a 0.01% of reference with a coverageData >= 27X
There is a 0.01% of reference with a coverageData >= 28X
There is a 0.01% of reference with a coverageData >= 29X
There is a 0.01% of reference with a coverageData >= 30X
There is a 0.01% of reference with a coverageData >= 31X
There is a 0.01% 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 94750689 0.38014223844200573 4.756347460815457
chr2 243199373 104442811 0.4294534550465309 2.748807354681276
chr3 198022430 101453761 0.5123346936001139 1.3887928970838692
chr4 191154276 56394974 0.2950233454364369 1.1316997982387194
chr5 180915260 51934312 0.2870642973953662 1.0077527091516323
chr6 171115067 61084142 0.3569769925637232 1.4089465842950741
chr7 159138663 82421879 0.5179249180948566 4.350457567603844
chr8 146364022 98280692 0.6714812196128362 5.075990079809781
chr9 141213431 36932842 0.2615391591186535 1.9621169860513026
chr10 135534747 33333580 0.2459412124036355 1.9304073164043811
chr11 135006516 45750355 0.3388751621440257 1.8262479669691367
chr12 133851895 39297596 0.2935901355748456 1.1114100543151695
chr13 115169878 33975371 0.29500223139942894 0.9938944181972539
chr14 107349540 42024036 0.39146917630014993 1.2030484378561401
chr15 102531392 30214766 0.29468795273939125 1.0543718175698404
chr16 90354753 21112668 0.23366416595704712 1.0033429704527423
chr17 81195210 22300952 0.2746584681534785 1.222620363218027
chr18 78077248 38025536 0.48702454266830714 3.73868661896703
chr19 59128983 19841620 0.33556504768566714 2.625172876447227
chr20 63025520 26332732 0.4178106265525457 1.368621796564265
chr21 48129895 16766681 0.3483631327265518 1.2593061548742177
chr22 51304566 9025013 0.17591052227203324 0.758008148193019
chrMT 16571 268784 16.22014362440408 10.252190613339845
chrX 155270560 35318212 0.22746238565765461 1.1008454346399212
chrY 59373566 2432405 0.04096781048994093 1.7031338563718854