BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716537.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 = 561,071 number of mapped reads = 493,840 (88.02%) number of supplementary alignments = 1,972 (0.35%) number of secondary alignments = 0 number of mapped bases = 28,438,382 bp number of sequenced bases = 28,430,111 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 9,856 duplication rate = 1.57% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.1309 >>>>>>> ACTG content number of A's = 7,335,446 bp (25.8%) number of C's = 5,291,053 bp (18.61%) number of T's = 9,192,573 bp (32.33%) number of G's = 6,610,246 bp (23.25%) number of N's = 793 bp (0%) GC percentage = 41.86% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 142,278 number of insertions = 2,103 mapped reads with insertion percentage = 0.42% number of deletions = 5,181 mapped reads with deletion percentage = 1.04% homopolymer indels = 42.85% >>>>>>> Coverage mean coverageData = 0.0092X std coverageData = 0.1167X There is a 0.87% 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 2229100 0.008943207407294684 0.17653435666564096 chr2 243199373 2425988 0.009975305322847194 0.13987764065493538 chr3 198022430 1898627 0.009587939103666185 0.10139876303296298 chr4 191154276 1806517 0.009450570700286088 0.1030248115262083 chr5 180915260 1649640 0.009118302126642053 0.09894103639949454 chr6 171115067 1624894 0.009495914231795848 0.1058771300797275 chr7 159138663 1528053 0.009602022357068564 0.12558344662982746 chr8 146364022 1423709 0.009727178718824767 0.11274983299728226 chr9 141213431 1201937 0.008511492083214096 0.10590337862427264 chr10 135534747 1512019 0.011155951027082375 0.12411464476563071 chr11 135006516 1252943 0.009280611315086451 0.10688660238332783 chr12 133851895 1256160 0.009384700903935651 0.10073908802345277 chr13 115169878 940776 0.008168594222180213 0.09343881837591937 chr14 107349540 880647 0.008203547029637947 0.09613819458156062 chr15 102531392 918757 0.008960738580433981 0.09841154683683437 chr16 90354753 788866 0.008730763726397438 0.1002088404779546 chr17 81195210 739243 0.009104514909192304 0.10018756150687455 chr18 78077248 756001 0.009682731133146496 0.14773688212438066 chr19 59128983 595563 0.010072268619942272 0.13585198321198683 chr20 63025520 628870 0.009978021601408446 0.10365136601689434 chr21 48129895 386526 0.008030892234441816 0.09594387823936606 chr22 51304566 329462 0.00642168964064524 0.0829178346703091 chrMT 16571 8031 0.4846418441856255 0.7479705462291196 chrX 155270560 1570254 0.010113018205125298 0.10734668570804388 chrY 59373566 85799 0.0014450706902125435 0.04831466889949575