BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR9716854.sorted.bam
outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 2,473,470
number of mapped reads = 2,320,489 (93.82%)
number of supplementary alignments = 47,696 (1.93%)
number of secondary alignments = 0
number of mapped bases = 180,292,883 bp
number of sequenced bases = 180,220,711 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 145,212
duplication rate = 4.82%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 46.6023
>>>>>>> ACTG content
number of A's = 43,285,748 bp (24.02%)
number of C's = 35,603,594 bp (19.76%)
number of T's = 55,229,337 bp (30.65%)
number of G's = 46,095,694 bp (25.58%)
number of N's = 6,338 bp (0%)
GC percentage = 45.33%
>>>>>>> Mismatches and indels
general error rate = 0.0068
number of mismatches = 1,186,509
number of insertions = 16,196
mapped reads with insertion percentage = 0.69%
number of deletions = 34,144
mapped reads with deletion percentage = 1.44%
homopolymer indels = 37.91%
>>>>>>> Coverage
mean coverageData = 0.0582X
std coverageData = 0.4625X
There is a 4.59% of reference with a coverageData >= 1X
There is a 0.82% of reference with a coverageData >= 2X
There is a 0.2% of reference with a coverageData >= 3X
There is a 0.06% of reference with a coverageData >= 4X
There is a 0.03% of reference with a coverageData >= 5X
There is a 0.01% of reference with a coverageData >= 6X
There is a 0.01% of reference with a coverageData >= 7X
There is a 0.01% of reference with a coverageData >= 8X
There is a 0.01% 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 20918699 0.08392636662678565 0.9534224124407609
chr2 243199373 15709045 0.06459327919402161 0.485840658096374
chr3 198022430 12176937 0.06149271574942293 0.3077843434973674
chr4 191154276 8770541 0.04588200266051072 0.4234070810379013
chr5 180915260 10257847 0.05669973334477147 0.2954039946514628
chr6 171115067 11504028 0.06722977819364089 0.3387587353972419
chr7 159138663 6229377 0.03914433414587629 0.3389313675099599
chr8 146364022 9345874 0.06385362927509604 0.4107387350719972
chr9 141213431 5642819 0.039959506401342236 0.32334437262656296
chr10 135534747 10135850 0.07478414372957808 0.6882971063794391
chr11 135006516 7976564 0.05908280752908252 0.38096871437063573
chr12 133851895 7038549 0.05258460479771317 0.2821148359397492
chr13 115169878 3553238 0.03085214694765935 0.211406042319983
chr14 107349540 3474821 0.03236922114431045 0.2460943221784516
chr15 102531392 3878811 0.03783047244691655 0.23581005534233326
chr16 90354753 5710645 0.06320248587254729 0.34229758980564956
chr17 81195210 3576826 0.04405217992539215 0.3036847307606726
chr18 78077248 5559954 0.07121093714778472 0.5108943819646828
chr19 59128983 4651153 0.07866113645147592 0.679860700661053
chr20 63025520 5228869 0.08296431350348239 0.3870338019566277
chr21 48129895 3347055 0.06954212137799179 0.42315107667586643
chr22 51304566 3036379 0.059183406794631105 0.32373909589025623
chrMT 16571 13003 0.7846840866574135 1.1399264162560327
chrX 155270560 11917704 0.0767544343241887 0.3630832654086373
chrY 59373566 638295 0.010750491220284798 0.4053257024365131