BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR9716239.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 = 1,370,124
number of mapped reads = 1,253,280 (91.47%)
number of supplementary alignments = 19,102 (1.39%)
number of secondary alignments = 0
number of mapped bases = 99,630,959 bp
number of sequenced bases = 99,587,288 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 47,684
duplication rate = 2.39%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 45.6406
>>>>>>> ACTG content
number of A's = 24,466,117 bp (24.57%)
number of C's = 18,334,130 bp (18.41%)
number of T's = 31,882,905 bp (32.02%)
number of G's = 24,898,176 bp (25%)
number of N's = 5,960 bp (0.01%)
GC percentage = 43.41%
>>>>>>> Mismatches and indels
general error rate = 0.0084
number of mismatches = 814,378
number of insertions = 8,880
mapped reads with insertion percentage = 0.7%
number of deletions = 24,745
mapped reads with deletion percentage = 1.94%
homopolymer indels = 45.18%
>>>>>>> Coverage
mean coverageData = 0.0322X
std coverageData = 0.3569X
There is a 2.83% of reference with a coverageData >= 1X
There is a 0.26% 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 0.01% 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 7835184 0.03143496280396429 0.5164186372841532
chr2 243199373 8523316 0.035046619959830244 0.5113324429504931
chr3 198022430 6593233 0.03329538477030102 0.20253406349596254
chr4 191154276 6414168 0.033554928167026724 0.22362691437579962
chr5 180915260 5996595 0.03314587724661811 0.20392576323491507
chr6 171115067 5710006 0.03336939347369101 0.2426548719157648
chr7 159138663 5496389 0.034538363565364376 0.4428140983062143
chr8 146364022 5093102 0.034797499620501 0.4853505581579696
chr9 141213431 4247723 0.030080162842300744 0.4030767653975526
chr10 135534747 4732000 0.03491355615250457 0.3635207840817286
chr11 135006516 4529416 0.0335496103017724 0.34829530162613453
chr12 133851895 4551790 0.03400616778716506 0.20658784323922993
chr13 115169878 3093807 0.026862987559993768 0.1789448947942876
chr14 107349540 3001147 0.02795677559493967 0.24068214811858418
chr15 102531392 2833315 0.027633634389748654 0.18536439397742313
chr16 90354753 2899152 0.03208632533144106 0.23105813612596013
chr17 81195210 2688994 0.033117643269843136 0.22718831415810314
chr18 78077248 2822109 0.03614508800310175 0.7866238515266185
chr19 59128983 2030610 0.03434204170229006 0.406845205522519
chr20 63025520 2033978 0.03227229223971496 0.2085097387684252
chr21 48129895 1313209 0.02728468449806508 0.19724773185217792
chr22 51304566 1128615 0.021998334417252453 0.1629066385520275
chrMT 16571 6765 0.40824331663749924 0.6991996926367253
chrX 155270560 5774813 0.037191937737585286 0.2837881622661638
chrY 59373566 281523 0.004741554516028227 0.15116964092692592