BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716546.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 = 709,303 number of mapped reads = 640,323 (90.27%) number of supplementary alignments = 2,286 (0.32%) number of secondary alignments = 0 number of mapped bases = 36,927,547 bp number of sequenced bases = 36,916,721 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 18,042 duplication rate = 2.22% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.0495 >>>>>>> ACTG content number of A's = 8,782,877 bp (23.79%) number of C's = 7,163,645 bp (19.4%) number of T's = 12,232,503 bp (33.14%) number of G's = 8,736,647 bp (23.67%) number of N's = 1,049 bp (0%) GC percentage = 43.07% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 186,833 number of insertions = 2,606 mapped reads with insertion percentage = 0.41% number of deletions = 7,000 mapped reads with deletion percentage = 1.08% homopolymer indels = 43.07% >>>>>>> Coverage mean coverageData = 0.0119X std coverageData = 0.143X There is a 1.12% 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 3231850 0.012966266591568493 0.23734506532207572 chr2 243199373 3024935 0.012438087165627684 0.1814501385397211 chr3 198022430 2462878 0.012437368837459474 0.11723815750615395 chr4 191154276 2367511 0.012385341565678604 0.1210907831381491 chr5 180915260 2204438 0.012184920166491206 0.11652298233421741 chr6 171115067 1987190 0.011613179568810268 0.12094680573292588 chr7 159138663 2172057 0.013648832779247366 0.15795624865303673 chr8 146364022 1872697 0.012794790512110962 0.1392249495519975 chr9 141213431 1500786 0.010627785114859224 0.11990826350981612 chr10 135534747 1827591 0.013484298605729497 0.14070253125043042 chr11 135006516 1672257 0.012386491034254968 0.1265610269408391 chr12 133851895 1676621 0.012525941451930882 0.118965324472069 chr13 115169878 1115024 0.00968155927021126 0.10287056970134428 chr14 107349540 1136539 0.010587274058184134 0.11072715711318372 chr15 102531392 1047996 0.010221220833517992 0.10690180711730225 chr16 90354753 1046140 0.011578140222462896 0.11647718849922631 chr17 81195210 1016870 0.012523768335595166 0.12216764311261084 chr18 78077248 924476 0.011840530035075007 0.17595570899849605 chr19 59128983 754198 0.012755132284280959 0.17688658924349315 chr20 63025520 782288 0.012412241898202506 0.11790945350999331 chr21 48129895 470073 0.009766757230615193 0.10752922364565282 chr22 51304566 464854 0.009060675028417549 0.1000798054369566 chrMT 16571 17225 1.039466537927705 1.2095466833712083 chrX 155270560 2031260 0.013082067843382545 0.12687457525390275 chrY 59373566 119793 0.0020176150443785034 0.06849508471963066