BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716483.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 = 604,305 number of mapped reads = 486,613 (80.52%) number of supplementary alignments = 1,573 (0.26%) number of secondary alignments = 0 number of mapped bases = 27,468,204 bp number of sequenced bases = 27,459,555 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 7,779 duplication rate = 1.11% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.6535 >>>>>>> ACTG content number of A's = 6,574,873 bp (23.94%) number of C's = 5,171,406 bp (18.83%) number of T's = 8,803,275 bp (32.06%) number of G's = 6,909,556 bp (25.16%) number of N's = 445 bp (0%) GC percentage = 44% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 141,634 number of insertions = 1,825 mapped reads with insertion percentage = 0.37% number of deletions = 5,437 mapped reads with deletion percentage = 1.11% homopolymer indels = 41.17% >>>>>>> Coverage mean coverageData = 0.0089X std coverageData = 0.1171X There is a 0.85% of reference with a coverageData >= 1X There is a 0.03% of reference with a coverageData >= 2X There is a 0% 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 2044032 0.008200709758713098 0.11981764571960658 chr2 243199373 2485712 0.010220881613868306 0.14601456925540937 chr3 198022430 2138645 0.010800013917615292 0.10987116041145631 chr4 191154276 1585429 0.008293976118012657 0.09536439464735562 chr5 180915260 1489549 0.008233407176376387 0.09325371213112885 chr6 171115067 1555857 0.009092460572159903 0.1029211832600801 chr7 159138663 1735370 0.01090476674420722 0.21928503591318815 chr8 146364022 2152573 0.014706981747194677 0.13440735029333548 chr9 141213431 1132525 0.008019952436393958 0.09654329448632094 chr10 135534747 1300810 0.00959761263286971 0.13980656678117453 chr11 135006516 938835 0.006953997687044972 0.09319208652428794 chr12 133851895 1300014 0.00971233167823287 0.10401521876119937 chr13 115169878 731907 0.006355021058544492 0.08271271700325822 chr14 107349540 698874 0.006510265437560329 0.08423521954129168 chr15 102531392 657285 0.006410573261309083 0.08337155221259519 chr16 90354753 837493 0.009268942387568698 0.1016644496368122 chr17 81195210 1124382 0.013847885854350275 0.12278185492715687 chr18 78077248 652253 0.008353944544766742 0.11892922807655436 chr19 59128983 563766 0.009534512034478929 0.13289019023025117 chr20 63025520 608022 0.00964723496132995 0.10159562204724362 chr21 48129895 278790 0.005792449786146427 0.07878450707699607 chr22 51304566 385042 0.007505024016770749 0.0895993552530277 chrMT 16571 12129 0.7319413433106029 0.9864880146881994 chrX 155270560 999045 0.006434220369914296 0.08827910564024001 chrY 59373566 59865 0.0010082769830601045 0.037435186302246924