BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR6236125.sorted.bam
outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 1,596,021
number of mapped reads = 1,382,204 (86.6%)
number of supplementary alignments = 8,254 (0.52%)
number of secondary alignments = 0
number of mapped bases = 90,733,844 bp
number of sequenced bases = 90,683,087 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 59,199
duplication rate = 3.31%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 43.7644
>>>>>>> ACTG content
number of A's = 24,707,501 bp (27.25%)
number of C's = 16,435,947 bp (18.12%)
number of T's = 28,972,977 bp (31.95%)
number of G's = 20,527,921 bp (22.64%)
number of N's = 38,741 bp (0.04%)
GC percentage = 40.76%
>>>>>>> Mismatches and indels
general error rate = 0.0085
number of mismatches = 757,177
number of insertions = 6,662
mapped reads with insertion percentage = 0.48%
number of deletions = 29,113
mapped reads with deletion percentage = 2.08%
homopolymer indels = 46.09%
>>>>>>> Coverage
mean coverageData = 0.0293X
std coverageData = 0.3279X
There is a 2.55% of reference with a coverageData >= 1X
There is a 0.27% of reference with a coverageData >= 2X
There is a 0.04% of reference with a coverageData >= 3X
There is a 0.01% of reference with a coverageData >= 4X
There is a 0% 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 8041964 0.032264569563499705 0.5916995037483704
chr2 243199373 4849668 0.01994112048964863 0.26971078911944923
chr3 198022430 6133422 0.030973370036919554 0.194387244753297
chr4 191154276 4709671 0.024638062504026854 0.19187454631992423
chr5 180915260 4814562 0.02661224929284572 0.18272420328228647
chr6 171115067 10242620 0.05985808368353676 0.4140780730670245
chr7 159138663 8405176 0.05281668100981846 0.6258234464192898
chr8 146364022 5224645 0.035696238246308916 0.5073125716020004
chr9 141213431 4088661 0.02895376856894016 0.24279834976211379
chr10 135534747 4118420 0.030386451379881205 0.2635682208023728
chr11 135006516 3777489 0.027980049496277647 0.2211543528008613
chr12 133851895 3477935 0.02598345731302497 0.18245883827027864
chr13 115169878 2858077 0.024816185009764447 0.173795240540358
chr14 107349540 1827879 0.01702735754619908 0.15081949695640415
chr15 102531392 3080081 0.03004037046527175 0.19716133833767438
chr16 90354753 4150772 0.04593861265936945 0.24854334106089182
chr17 81195210 1931223 0.023784937559740284 0.19998649742895822
chr18 78077248 1441207 0.01845873204957224 0.37556016512067625
chr19 59128983 1947640 0.03293883813290007 0.4169569708020233
chr20 63025520 1475726 0.02341473739526465 0.17416515038866057
chr21 48129895 861493 0.017899332628920135 0.16608366910766895
chr22 51304566 597453 0.011645220817188084 0.11735692946860839
chrMT 16571 70652 4.263593023957516 3.2310028088133755
chrX 155270560 2396539 0.015434600094183985 0.15174054151116032
chrY 59373566 210869 0.0035515636706072193 0.10688609549724319