BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524989.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 = 1,297,844 number of mapped reads = 1,144,529 (88.19%) number of supplementary alignments = 4,368 (0.34%) number of secondary alignments = 0 number of mapped bases = 65,346,420 bp number of sequenced bases = 65,329,957 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 26,361 duplication rate = 1.59% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.5761 >>>>>>> ACTG content number of A's = 16,956,518 bp (25.96%) number of C's = 12,115,555 bp (18.55%) number of T's = 21,008,986 bp (32.16%) number of G's = 15,246,908 bp (23.34%) number of N's = 1,990 bp (0%) GC percentage = 41.88% >>>>>>> Mismatches and indels general error rate = 0.0049 number of mismatches = 311,447 number of insertions = 4,831 mapped reads with insertion percentage = 0.42% number of deletions = 9,791 mapped reads with deletion percentage = 0.85% homopolymer indels = 41.98% >>>>>>> Coverage mean coverageData = 0.0211X std coverageData = 0.2061X There is a 1.95% of reference with a coverageData >= 1X There is a 0.11% of reference with a coverageData >= 2X There is a 0.01% 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 4795749 0.01924067021682566 0.32289929442259274 chr2 243199373 5749628 0.02364162345106046 0.2308102209399018 chr3 198022430 4028802 0.020345180088942448 0.14994863317777415 chr4 191154276 4144068 0.02167918022404061 0.16683175511967005 chr5 180915260 3676003 0.020318921687424267 0.15173185481366494 chr6 171115067 3636453 0.0212515067419516 0.16630529405984576 chr7 159138663 4271206 0.026839524220459234 0.27772397970942897 chr8 146364022 2906007 0.01985465389848333 0.19491083994566366 chr9 141213431 2444724 0.01731226259915744 0.2046044913698373 chr10 135534747 2499158 0.018439242004856513 0.19930732310408256 chr11 135006516 2373366 0.017579640378246632 0.1766833320396891 chr12 133851895 3901389 0.029147058396147472 0.19994226172740767 chr13 115169878 2548210 0.022125663795528203 0.15657036059754534 chr14 107349540 2395159 0.022311777022984914 0.1674524722172672 chr15 102531392 1739634 0.01696684270120901 0.13830247633699877 chr16 90354753 1829208 0.020244734662713315 0.15859962864128674 chr17 81195210 1970311 0.02426634526839699 0.16880659264356498 chr18 78077248 2164976 0.02772864125538851 0.34636625966920215 chr19 59128983 1085118 0.018351710869101198 0.254186825708419 chr20 63025520 2026392 0.032151928298251246 0.19467924797404776 chr21 48129895 798906 0.016598955804910855 0.1490288968477193 chr22 51304566 638519 0.012445656396352714 0.1175162516991946 chrMT 16571 2386 0.1439864824090278 0.4272171913351905 chrX 155270560 3536928 0.022779128252000895 0.17818420557399625 chrY 59373566 184120 0.0031010433161451005 0.0819990454448685