BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716292.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 = 1,336,570 number of mapped reads = 1,095,990 (82%) number of supplementary alignments = 3,091 (0.23%) number of secondary alignments = 0 number of mapped bases = 60,831,969 bp number of sequenced bases = 60,815,716 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 25,646 duplication rate = 1.71% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 39.2469 >>>>>>> ACTG content number of A's = 13,883,494 bp (22.83%) number of C's = 12,461,984 bp (20.49%) number of T's = 18,531,535 bp (30.47%) number of G's = 15,937,252 bp (26.21%) number of N's = 1,451 bp (0%) GC percentage = 46.7% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 314,127 number of insertions = 4,273 mapped reads with insertion percentage = 0.39% number of deletions = 9,596 mapped reads with deletion percentage = 0.87% homopolymer indels = 36.92% >>>>>>> Coverage mean coverageData = 0.0197X std coverageData = 0.1767X There is a 1.77% of reference with a coverageData >= 1X There is a 0.14% of reference with a coverageData >= 2X There is a 0.02% of reference with a coverageData >= 3X There is a 0.01% 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 6265437 0.025137096850001428 0.22488595224898036 chr2 243199373 5203013 0.021394023084097342 0.22030590914912607 chr3 198022430 3762317 0.018999448698816594 0.15733703621023287 chr4 191154276 4409766 0.02306914651493331 0.185251650890005 chr5 180915260 3852348 0.021293659805148555 0.16029336471673722 chr6 171115067 2628315 0.015359927363964975 0.13952938290213784 chr7 159138663 3502393 0.02200843549879516 0.1989576333061334 chr8 146364022 3989317 0.027256131291609354 0.1937483643609457 chr9 141213431 2038269 0.014433959897199863 0.1412707268765524 chr10 135534747 3232292 0.02384843792123654 0.2259306201997701 chr11 135006516 2445124 0.018111155464525876 0.17695602560245155 chr12 133851895 2912621 0.021760028126609637 0.1629256705035445 chr13 115169878 1069587 0.009287037709634459 0.10565488098268258 chr14 107349540 1911840 0.017809484791457886 0.1495899402047922 chr15 102531392 1185512 0.011562429582541901 0.12056767057087582 chr16 90354753 1750866 0.019377685643166994 0.16223367505063485 chr17 81195210 2404411 0.029612719765119148 0.19818686971801333 chr18 78077248 1747985 0.02238789205275268 0.18776228470278247 chr19 59128983 1239056 0.02095513802427483 0.19649581510723288 chr20 63025520 1561092 0.024769204601564572 0.18228483364617518 chr21 48129895 791875 0.016452871962425848 0.155950399176654 chr22 51304566 533498 0.010398645609827398 0.11445494234503852 chrMT 16571 9796 0.5911532194798141 0.888553096228092 chrX 155270560 2191140 0.014111754346735145 0.14032574633494177 chrY 59373566 194099 0.003269114743756506 0.10137913289190961