BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR617398.sorted.bam
outfile = /home/luna/rawdata/yangyxdownload/SRP017032/SRP017032.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 = 32,000,000
number of mapped reads = 29,204,957 (91.27%)
number of supplementary alignments = 422,632 (1.32%)
number of secondary alignments = 0
number of mapped paired reads (first in pair) = 14,725,944
number of mapped paired reads (second in pair) = 14,479,013
number of mapped paired reads (both in pair) = 28,600,472
number of mapped paired reads (singletons) = 604,485
number of mapped bases = 2,863,228,294 bp
number of sequenced bases = 2,862,619,790 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 1,289,899
duplication rate = 4.04%
>>>>>>> Insert size
mean insert size = 47,564.1508
std insert size = 2,074,007.5552
median insert size = 205
>>>>>>> Mapping quality
mean mapping quality = 53.8279
>>>>>>> ACTG content
number of A's = 856,326,439 bp (29.91%)
number of C's = 573,376,361 bp (20.03%)
number of T's = 845,475,564 bp (29.54%)
number of G's = 585,675,028 bp (20.46%)
number of N's = 1,766,398 bp (0.06%)
GC percentage = 40.49%
>>>>>>> Mismatches and indels
general error rate = 0.0139
number of mismatches = 39,358,606
number of insertions = 233,246
mapped reads with insertion percentage = 0.79%
number of deletions = 272,754
mapped reads with deletion percentage = 0.91%
homopolymer indels = 44.17%
>>>>>>> Coverage
mean coverageData = 0.9249X
std coverageData = 2.8231X
There is a 29.16% of reference with a coverageData >= 1X
There is a 16.64% of reference with a coverageData >= 2X
There is a 10.59% of reference with a coverageData >= 3X
There is a 7.29% of reference with a coverageData >= 4X
There is a 5.27% of reference with a coverageData >= 5X
There is a 3.96% of reference with a coverageData >= 6X
There is a 3.05% of reference with a coverageData >= 7X
There is a 2.41% of reference with a coverageData >= 8X
There is a 1.93% of reference with a coverageData >= 9X
There is a 1.58% of reference with a coverageData >= 10X
There is a 1.3% of reference with a coverageData >= 11X
There is a 1.09% of reference with a coverageData >= 12X
There is a 0.92% of reference with a coverageData >= 13X
There is a 0.78% of reference with a coverageData >= 14X
There is a 0.67% of reference with a coverageData >= 15X
There is a 0.58% of reference with a coverageData >= 16X
There is a 0.5% of reference with a coverageData >= 17X
There is a 0.44% of reference with a coverageData >= 18X
There is a 0.39% of reference with a coverageData >= 19X
There is a 0.34% of reference with a coverageData >= 20X
There is a 0.3% of reference with a coverageData >= 21X
There is a 0.27% of reference with a coverageData >= 22X
There is a 0.24% of reference with a coverageData >= 23X
There is a 0.21% of reference with a coverageData >= 24X
There is a 0.19% of reference with a coverageData >= 25X
There is a 0.17% of reference with a coverageData >= 26X
There is a 0.16% of reference with a coverageData >= 27X
There is a 0.14% of reference with a coverageData >= 28X
There is a 0.13% of reference with a coverageData >= 29X
There is a 0.12% of reference with a coverageData >= 30X
There is a 0.11% of reference with a coverageData >= 31X
There is a 0.1% of reference with a coverageData >= 32X
There is a 0.09% of reference with a coverageData >= 33X
There is a 0.08% of reference with a coverageData >= 34X
There is a 0.07% of reference with a coverageData >= 35X
There is a 0.07% of reference with a coverageData >= 36X
There is a 0.06% of reference with a coverageData >= 37X
There is a 0.06% of reference with a coverageData >= 38X
There is a 0.05% of reference with a coverageData >= 39X
There is a 0.05% of reference with a coverageData >= 40X
There is a 0.05% of reference with a coverageData >= 41X
There is a 0.04% of reference with a coverageData >= 42X
There is a 0.04% of reference with a coverageData >= 43X
There is a 0.04% of reference with a coverageData >= 44X
There is a 0.04% of reference with a coverageData >= 45X
There is a 0.03% of reference with a coverageData >= 46X
There is a 0.03% of reference with a coverageData >= 47X
There is a 0.03% of reference with a coverageData >= 48X
There is a 0.03% of reference with a coverageData >= 49X
There is a 0.03% of reference with a coverageData >= 50X
There is a 0.02% of reference with a coverageData >= 51X
>>>>>>> Coverage per contig
chr1 249250621 184427069 0.7399262166732977 2.643975593200771
chr2 243199373 285563746 1.1741960617636955 2.9683492701162812
chr3 198022430 241520276 1.2196612070662904 3.2873380028270045
chr4 191154276 138999903 0.7271608352616711 2.228086862408201
chr5 180915260 183819461 1.0160528249524114 2.7889775088712345
chr6 171115067 131642218 0.769319851886567 2.5220878055575975
chr7 159138663 214633777 1.348721755944374 3.137369849322208
chr8 146364022 126752254 0.866006907079938 3.118660025933495
chr9 141213431 114373306 0.8099322082189193 2.5181321234787832
chr10 135534747 91723019 0.676749107002059 2.3257095763473132
chr11 135006516 212363973 1.5729905436564262 3.708694826659479
chr12 133851895 136110179 1.0168715131003563 2.683512223462701
chr13 115169878 124690166 1.08266300325507 2.6822919615770284
chr14 107349540 83014615 0.7733113248552346 2.793335155626134
chr15 102531392 65673104 0.6405170428194323 2.285958740092089
chr16 90354753 71600020 0.7924322475874622 3.2012538130498194
chr17 81195210 87381848 1.0761946178844786 3.5402863294918756
chr18 78077248 41209211 0.5278005059809485 1.9392592067287036
chr19 59128983 40379763 0.6829098176777368 2.2291361062155044
chr20 63025520 96762033 1.5352833740998884 4.515507347325066
chr21 48129895 39311273 0.8167745431399757 2.4551845758050725
chr22 51304566 22834584 0.44507898185904154 2.0039005837881176
chrMT 16571 167795 10.12582221954016 5.307076300012331
chrX 155270560 125978723 0.811349704670351 2.4863878386420137
chrY 59373566 2295978 0.038670037100348664 0.5496679998297744