BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR10525277.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 = 843,049
number of mapped reads = 753,829 (89.42%)
number of supplementary alignments = 3,302 (0.39%)
number of secondary alignments = 0
number of mapped bases = 43,703,837 bp
number of sequenced bases = 43,689,578 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 18,377
duplication rate = 1.83%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 45.1214
>>>>>>> ACTG content
number of A's = 10,902,109 bp (24.95%)
number of C's = 7,951,398 bp (18.2%)
number of T's = 14,345,213 bp (32.83%)
number of G's = 10,489,957 bp (24.01%)
number of N's = 901 bp (0%)
GC percentage = 42.21%
>>>>>>> Mismatches and indels
general error rate = 0.0051
number of mismatches = 219,201
number of insertions = 3,083
mapped reads with insertion percentage = 0.41%
number of deletions = 8,857
mapped reads with deletion percentage = 1.17%
homopolymer indels = 42.91%
>>>>>>> Coverage
mean coverageData = 0.0141X
std coverageData = 0.1617X
There is a 1.33% of reference with a coverageData >= 1X
There is a 0.06% of reference with a coverageData >= 2X
There is a 0.01% of reference with a coverageData >= 3X
There is a 0% 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 4628621 0.018570148316701687 0.2897871331616464
chr2 243199373 4095641 0.01684067252920097 0.19497251979324126
chr3 198022430 3600559 0.018182581639867766 0.14140112561399773
chr4 191154276 2705005 0.014150899768519958 0.12722528435459401
chr5 180915260 2018504 0.011157179333573077 0.11031311773021443
chr6 171115067 2219016 0.012967975520238671 0.129878222807844
chr7 159138663 2525487 0.01586972613939832 0.1897528937368302
chr8 146364022 2198345 0.01501970887353724 0.15825824608724623
chr9 141213431 1451702 0.010280197780903716 0.12494005438445142
chr10 135534747 2256660 0.016650047681130802 0.1812264791767744
chr11 135006516 2142490 0.015869530326965847 0.14526509273178415
chr12 133851895 2211227 0.01651995289271026 0.13485515315874866
chr13 115169878 1467622 0.012743106318129468 0.1182289697827379
chr14 107349540 1660883 0.01547172908239756 0.1313128737638093
chr15 102531392 1238803 0.012082182596331082 0.11594264951768568
chr16 90354753 1094764 0.012116285681174958 0.12330843912625562
chr17 81195210 879664 0.010833939588308226 0.11101306572513779
chr18 78077248 912187 0.011683134630974699 0.2111215812926006
chr19 59128983 693587 0.011730068146106961 0.189613349226191
chr20 63025520 752438 0.011938624227138468 0.11557774237832477
chr21 48129895 547357 0.011372495202825603 0.11439073042049737
chr22 51304566 302964 0.005905205396338408 0.07998796613629772
chrMT 16571 1134 0.06843280429666285 0.2567532386756384
chrX 155270560 1976341 0.012728369112599324 0.12387451000068274
chrY 59373566 122836 0.0020688668085053204 0.06758307946257384