BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR3081775.sorted.bam
outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 2,170,735
number of mapped reads = 1,983,795 (91.39%)
number of supplementary alignments = 13,447 (0.62%)
number of secondary alignments = 0
number of mapped bases = 133,626,287 bp
number of sequenced bases = 133,578,076 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 77,071
duplication rate = 3.08%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 46.2411
>>>>>>> ACTG content
number of A's = 37,048,121 bp (27.74%)
number of C's = 25,212,263 bp (18.87%)
number of T's = 41,754,013 bp (31.26%)
number of G's = 29,562,163 bp (22.13%)
number of N's = 1,516 bp (0%)
GC percentage = 41.01%
>>>>>>> Mismatches and indels
general error rate = 0.0078
number of mismatches = 1,019,473
number of insertions = 9,445
mapped reads with insertion percentage = 0.47%
number of deletions = 27,001
mapped reads with deletion percentage = 1.35%
homopolymer indels = 47.17%
>>>>>>> Coverage
mean coverageData = 0.0432X
std coverageData = 0.3392X
There is a 3.71% of reference with a coverageData >= 1X
There is a 0.45% of reference with a coverageData >= 2X
There is a 0.07% of reference with a coverageData >= 3X
There is a 0.02% of reference with a coverageData >= 4X
There is a 0.01% of reference with a coverageData >= 5X
There is a 0% of reference with a coverageData >= 6X
There is a 0% of reference with a coverageData >= 7X
There is a 0% of reference with a coverageData >= 8X
There is a 0% of reference with a coverageData >= 9X
There is a 0% of reference with a coverageData >= 10X
There is a 0% of reference with a coverageData >= 11X
There is a 0% of reference with a coverageData >= 12X
There is a 0% of reference with a coverageData >= 13X
There is a 0% of reference with a coverageData >= 14X
There is a 0% of reference with a coverageData >= 15X
There is a 0% of reference with a coverageData >= 16X
There is a 0% of reference with a coverageData >= 17X
There is a 0% of reference with a coverageData >= 18X
There is a 0% of reference with a coverageData >= 19X
There is a 0% of reference with a coverageData >= 20X
There is a 0% of reference with a coverageData >= 21X
There is a 0% of reference with a coverageData >= 22X
There is a 0% 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 9845686 0.03950114932712645 0.4969539905353606
chr2 243199373 11767883 0.04838780155901142 0.43109064803778263
chr3 198022430 8664889 0.043757108727531524 0.23617465569717458
chr4 191154276 9453040 0.049452411935582336 0.2680013133858257
chr5 180915260 9341339 0.05163378147316042 0.2566617573258467
chr6 171115067 7433598 0.043442100864209694 0.2679152128947694
chr7 159138663 7154871 0.04495997933575702 0.4248356997530278
chr8 146364022 6898825 0.04713470500284558 0.4569632980680514
chr9 141213431 5475643 0.03877565300428116 0.347470672086851
chr10 135534747 6337465 0.0467589687535994 0.3533966388016024
chr11 135006516 5658734 0.04191452507373792 0.30520514468256793
chr12 133851895 5718177 0.04272017964332892 0.23473069029991697
chr13 115169878 4722736 0.041006694476137244 0.22702475096723754
chr14 107349540 3967932 0.036962729416446495 0.2314169148833123
chr15 102531392 3893168 0.03797049785493988 0.22144830675422908
chr16 90354753 3762169 0.04163775424188255 0.2608875801932205
chr17 81195210 3291407 0.04053696024679288 0.24096275458607472
chr18 78077248 4028738 0.051599385265218366 0.593590838278366
chr19 59128983 2328444 0.0393790639017079 0.4325991600961184
chr20 63025520 2661974 0.04223644644264736 0.23994373591465645
chr21 48129895 1730799 0.03596099679835163 0.2336337643756269
chr22 51304566 1426757 0.02780955207768447 0.18693037581648997
chrMT 16571 19901 1.200953472934645 1.4582936644199946
chrX 155270560 7693484 0.049548890658989056 0.2762020052753144
chrY 59373566 348628 0.005871771286231991 0.13231037094502504