BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524811.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 = 990,561 number of mapped reads = 908,216 (91.69%) number of supplementary alignments = 3,086 (0.31%) number of secondary alignments = 0 number of mapped bases = 52,703,942 bp number of sequenced bases = 52,686,243 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 23,478 duplication rate = 1.88% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.9119 >>>>>>> ACTG content number of A's = 13,568,796 bp (25.75%) number of C's = 10,473,398 bp (19.88%) number of T's = 16,337,590 bp (31.01%) number of G's = 12,305,295 bp (23.36%) number of N's = 1,164 bp (0%) GC percentage = 43.23% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 264,686 number of insertions = 3,918 mapped reads with insertion percentage = 0.43% number of deletions = 11,108 mapped reads with deletion percentage = 1.21% homopolymer indels = 43.82% >>>>>>> Coverage mean coverageData = 0.017X std coverageData = 0.1857X There is a 1.59% of reference with a coverageData >= 1X There is a 0.08% of reference with a coverageData >= 2X There is a 0.01% 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 6061946 0.02432068564434991 0.3093692788476112 chr2 243199373 4329495 0.017802245731941092 0.22207356676954224 chr3 198022430 4095878 0.020683909393496486 0.1524809370017515 chr4 191154276 2981366 0.015596648227738312 0.1354897429132499 chr5 180915260 2366445 0.013080405710386177 0.12069219150518726 chr6 171115067 3261931 0.019062792407403845 0.15599994043097778 chr7 159138663 3847659 0.02417802768645857 0.3130980365781196 chr8 146364022 3058030 0.020893317621457547 0.18820803210387707 chr9 141213431 1712168 0.012124682389453452 0.13645071828462357 chr10 135534747 2808203 0.020719432191067578 0.21157494927563283 chr11 135006516 2384672 0.017663384484345925 0.1553368107028772 chr12 133851895 2362923 0.01765326520031711 0.14081005997879764 chr13 115169878 1650496 0.014330969422404007 0.1265414785656338 chr14 107349540 1510990 0.014075421282662226 0.12749697045380298 chr15 102531392 1402903 0.01368266803595137 0.12486763155066377 chr16 90354753 1385006 0.015328535068874573 0.140125643309137 chr17 81195210 1124640 0.01385106338169456 0.12642586280904652 chr18 78077248 1118145 0.014321009367543281 0.22054660286090824 chr19 59128983 912057 0.015424872096988375 0.22344091057310903 chr20 63025520 933665 0.014814078487571384 0.12789906255784253 chr21 48129895 674586 0.014015945806655095 0.12786256888194678 chr22 51304566 402024 0.007836027693909349 0.09201227874127181 chrMT 16571 39837 2.404019069458693 2.038059635941501 chrX 155270560 2134567 0.013747403242443383 0.13247740609099595 chrY 59373566 144310 0.0024305429119753394 0.07504798183605346