BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR10525011.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 = 1,808,542
number of mapped reads = 1,557,010 (86.09%)
number of supplementary alignments = 9,598 (0.53%)
number of secondary alignments = 0
number of mapped bases = 85,798,300 bp
number of sequenced bases = 85,763,971 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 209,085
duplication rate = 10.42%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 44.86
>>>>>>> ACTG content
number of A's = 20,811,344 bp (24.27%)
number of C's = 17,099,493 bp (19.94%)
number of T's = 27,822,862 bp (32.44%)
number of G's = 20,027,986 bp (23.35%)
number of N's = 2,286 bp (0%)
GC percentage = 43.29%
>>>>>>> Mismatches and indels
general error rate = 0.0059
number of mismatches = 497,150
number of insertions = 5,256
mapped reads with insertion percentage = 0.34%
number of deletions = 20,480
mapped reads with deletion percentage = 1.3%
homopolymer indels = 41.02%
>>>>>>> Coverage
mean coverageData = 0.0277X
std coverageData = 0.2991X
There is a 1.82% of reference with a coverageData >= 1X
There is a 0.57% of reference with a coverageData >= 2X
There is a 0.2% of reference with a coverageData >= 3X
There is a 0.08% of reference with a coverageData >= 4X
There is a 0.03% of reference with a coverageData >= 5X
There is a 0.02% 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% 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 6271616 0.025161887159350346 0.3862716455906349
chr2 243199373 6886342 0.0283156239880602 0.3381717605423252
chr3 198022430 5513967 0.02784516380290859 0.23687938976707604
chr4 191154276 5768318 0.030176243611730665 0.30386267349363894
chr5 180915260 4395239 0.0242944625013943 0.2213874200841066
chr6 171115067 4131273 0.024143245083146303 0.23191696656457222
chr7 159138663 5552891 0.03489341241983414 0.3550194416623899
chr8 146364022 3795279 0.025930409318760044 0.32080582097949484
chr9 141213431 3952199 0.027987415729598696 0.28909533549771094
chr10 135534747 3519450 0.02596714184296961 0.3550221497798717
chr11 135006516 3308916 0.024509305906390475 0.2501910083606637
chr12 133851895 5979109 0.04466958798005811 0.32157916226429656
chr13 115169878 3065216 0.026614736884587133 0.23281751775953796
chr14 107349540 2800356 0.02608633441745535 0.238554252607613
chr15 102531392 2000471 0.019510814795140986 0.19773414377502962
chr16 90354753 2439016 0.02699377640930522 0.24580768258884803
chr17 81195210 2612569 0.032176393164079505 0.2660614731003444
chr18 78077248 2491502 0.031910730255246704 0.4191855760062166
chr19 59128983 1471150 0.02488035351462074 0.3214580467282769
chr20 63025520 2615536 0.041499633799134066 0.30789271015937547
chr21 48129895 1169525 0.02429934659113634 0.2512440222363589
chr22 51304566 894240 0.01743002757298444 0.18713005157602158
chrMT 16571 296320 17.88184177176996 12.0152406622557
chrX 155270560 4538012 0.029226480538229526 0.26173614035258275
chrY 59373566 329788 0.0055544583594658945 0.1918189239799111