BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6234068.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 = 785,688 number of mapped reads = 605,956 (77.12%) number of supplementary alignments = 6,513 (0.83%) number of secondary alignments = 0 number of mapped bases = 38,853,656 bp number of sequenced bases = 38,827,560 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 44,497 duplication rate = 6.05% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.5349 >>>>>>> ACTG content number of A's = 10,805,549 bp (27.83%) number of C's = 6,557,325 bp (16.89%) number of T's = 13,135,567 bp (33.83%) number of G's = 8,327,073 bp (21.45%) number of N's = 2,046 bp (0.01%) GC percentage = 38.33% >>>>>>> Mismatches and indels general error rate = 0.0083 number of mismatches = 318,314 number of insertions = 3,098 mapped reads with insertion percentage = 0.51% number of deletions = 14,805 mapped reads with deletion percentage = 2.41% homopolymer indels = 42.84% >>>>>>> Coverage mean coverageData = 0.0126X std coverageData = 0.2142X There is a 0.99% of reference with a coverageData >= 1X There is a 0.19% of reference with a coverageData >= 2X There is a 0.04% 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 2620859 0.010514954745087676 0.24571015794886458 chr2 243199373 2139881 0.00879887548065348 0.17627727900722007 chr3 198022430 3797889 0.019179084914774554 0.1704171119313586 chr4 191154276 1087702 0.0056901787538354625 0.0964801332901294 chr5 180915260 2486471 0.013743843388335512 0.1448351037803493 chr6 171115067 2064214 0.012063309422074446 0.14073478310082668 chr7 159138663 2980500 0.018728949607927772 0.2549805468622986 chr8 146364022 1819880 0.012433929972216807 0.6243078010435203 chr9 141213431 1802666 0.012765542110509304 0.15216897975466648 chr10 135534747 1435099 0.010588421285059837 0.15006468709420404 chr11 135006516 2549931 0.018887466142745286 0.1939509082355366 chr12 133851895 2406632 0.017979812687747156 0.16752328634856611 chr13 115169878 2171764 0.018857048715463603 0.1717492037631004 chr14 107349540 1655244 0.0154191997469202 0.15592101593604601 chr15 102531392 510022 0.004974300943851421 0.08454960148970966 chr16 90354753 1254285 0.013881782179184309 0.149592277141194 chr17 81195210 721361 0.008884280242639929 0.11864759458682717 chr18 78077248 1025165 0.013130137476156947 0.2511042886254225 chr19 59128983 907185 0.015342475956334308 0.18139759965585248 chr20 63025520 736570 0.011686853198513873 0.1347312889171968 chr21 48129895 291171 0.006049691153492024 0.09603646455141562 chr22 51304566 410231 0.007995993962798554 0.10585927555014184 chrMT 16571 14061 0.8485305654456581 1.1845301782766091 chrX 155270560 1864866 0.012010428763830053 0.14002222457619481 chrY 59373566 100007 0.0016843691012259565 0.050590545708386524