BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6234151.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 2,586,777 number of mapped reads = 1,659,631 (64.16%) number of supplementary alignments = 16,915 (0.65%) number of secondary alignments = 0 number of mapped bases = 105,620,675 bp number of sequenced bases = 105,530,549 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 113,215 duplication rate = 5.76% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.3856 >>>>>>> ACTG content number of A's = 28,730,485 bp (27.22%) number of C's = 20,042,498 bp (18.99%) number of T's = 32,922,794 bp (31.2%) number of G's = 23,809,100 bp (22.56%) number of N's = 25,672 bp (0.02%) GC percentage = 41.55% >>>>>>> Mismatches and indels general error rate = 0.0093 number of mismatches = 965,644 number of insertions = 8,260 mapped reads with insertion percentage = 0.49% number of deletions = 51,346 mapped reads with deletion percentage = 3.03% homopolymer indels = 42.62% >>>>>>> Coverage mean coverageData = 0.0341X std coverageData = 0.3166X There is a 2.51% of reference with a coverageData >= 1X There is a 0.62% of reference with a coverageData >= 2X There is a 0.17% of reference with a coverageData >= 3X There is a 0.05% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.01% 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 8116667 0.03256427995017914 0.6016751471742176 chr2 243199373 8844406 0.03636689474524262 0.32590222136995745 chr3 198022430 8753862 0.04420641641454456 0.2737025785388982 chr4 191154276 6432812 0.03365246195172741 0.2455511268361396 chr5 180915260 5950058 0.03288864631982952 0.2369314590856151 chr6 171115067 5356808 0.03130529703734388 0.2631764040523255 chr7 159138663 4965092 0.031199784555183803 0.2962697640863247 chr8 146364022 4384578 0.029956665170078476 0.32025612061459 chr9 141213431 4853912 0.03437287774701827 0.2654912861517255 chr10 135534747 7518743 0.05547465256271147 0.35267867441908546 chr11 135006516 7069233 0.0523621615418918 0.33593138410963685 chr12 133851895 3449024 0.025767464853598075 0.21035722192930315 chr13 115169878 3773189 0.03276194318795753 0.24226717518494836 chr14 107349540 2777297 0.025871531447642905 0.22124632442944656 chr15 102531392 1765510 0.01721921418954304 0.17344502354867206 chr16 90354753 3031839 0.03355483689939366 0.24544355889975902 chr17 81195210 2854305 0.035153613125700395 0.2633079602892304 chr18 78077248 2099296 0.026887423081305324 0.35589985806216595 chr19 59128983 3743637 0.06331306256358239 0.5010374301620912 chr20 63025520 2357001 0.03739756530370555 0.25412689199177624 chr21 48129895 1958726 0.04069666056823935 0.267469816054394 chr22 51304566 1158590 0.02258259040725537 0.19308479328660028 chrMT 16571 38458 2.320801400036208 2.2649703800406478 chrX 155270560 4113899 0.026495035504476832 0.21959445574887634 chrY 59373566 253733 0.004273501106536198 0.10018520005239732