BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524784.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 = 1,269,437 number of mapped reads = 1,162,961 (91.61%) number of supplementary alignments = 4,017 (0.32%) number of secondary alignments = 0 number of mapped bases = 67,008,026 bp number of sequenced bases = 66,986,414 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 35,144 duplication rate = 2.27% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.821 >>>>>>> ACTG content number of A's = 16,804,331 bp (25.09%) number of C's = 12,496,191 bp (18.65%) number of T's = 20,407,029 bp (30.46%) number of G's = 17,270,874 bp (25.78%) number of N's = 7,989 bp (0.01%) GC percentage = 44.44% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 335,033 number of insertions = 4,292 mapped reads with insertion percentage = 0.37% number of deletions = 13,100 mapped reads with deletion percentage = 1.12% homopolymer indels = 42.27% >>>>>>> Coverage mean coverageData = 0.0216X std coverageData = 0.2008X There is a 1.97% 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 5372418 0.021554281303074466 0.2661407471190546 chr2 243199373 5651856 0.023239599388276383 0.28833829786488885 chr3 198022430 4381568 0.022126624746499676 0.16155681499363442 chr4 191154276 4253768 0.02225306223335543 0.1793193612554872 chr5 180915260 3985785 0.022031226111053317 0.15953368723785963 chr6 171115067 3826333 0.02236116939953628 0.1718076187181964 chr7 159138663 3659121 0.022993287306931818 0.24095354505352548 chr8 146364022 3301414 0.022556185289852173 0.18587753149079814 chr9 141213431 2865368 0.020291044412057375 0.1830051063797248 chr10 135534747 3291858 0.024287926696760647 0.2436709767854213 chr11 135006516 3014405 0.022327848235117777 0.18568540645593265 chr12 133851895 3004269 0.02244472519421559 0.16202971215171458 chr13 115169878 2084391 0.01809840416779811 0.1445171257236002 chr14 107349540 2012087 0.018743322048701837 0.14965467935435933 chr15 102531392 1950044 0.019018994689938472 0.148905507652605 chr16 90354753 2058943 0.022787323650810046 0.17527124298010702 chr17 81195210 1910887 0.023534479435424825 0.1732964798602858 chr18 78077248 1769902 0.022668601229387592 0.27481252032063724 chr19 59128983 1457764 0.0246539670739813 0.22233254678981323 chr20 63025520 1459830 0.02316252210215798 0.16920413449751973 chr21 48129895 881211 0.018309015633630615 0.15846845017764033 chr22 51304566 855160 0.016668301998695397 0.13973969404888364 chrMT 16571 28237 1.7040009655422124 1.6513639457360478 chrX 155270560 3706879 0.023873675730930577 0.17520731277100313 chrY 59373566 224528 0.0037816155425126393 0.11212947194495933