BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6008774.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 = 2,096,221 number of mapped reads = 1,429,970 (68.22%) number of supplementary alignments = 6,468 (0.31%) number of secondary alignments = 0 number of mapped bases = 83,609,015 bp number of sequenced bases = 83,563,226 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 100,967 duplication rate = 5.93% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.5427 >>>>>>> ACTG content number of A's = 24,711,852 bp (29.57%) number of C's = 16,064,899 bp (19.22%) number of T's = 24,645,783 bp (29.49%) number of G's = 18,127,371 bp (21.69%) number of N's = 13,321 bp (0.02%) GC percentage = 40.92% >>>>>>> Mismatches and indels general error rate = 0.0097 number of mismatches = 798,766 number of insertions = 6,740 mapped reads with insertion percentage = 0.47% number of deletions = 29,917 mapped reads with deletion percentage = 2.07% homopolymer indels = 47.49% >>>>>>> Coverage mean coverageData = 0.027X std coverageData = 0.2708X There is a 1.99% of reference with a coverageData >= 1X There is a 0.48% of reference with a coverageData >= 2X There is a 0.13% of reference with a coverageData >= 3X There is a 0.04% of reference with a coverageData >= 4X There is a 0.01% 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 6526169 0.02618316044235653 0.31798449880637725 chr2 243199373 6809839 0.028001054920482875 0.2970209116737946 chr3 198022430 6131953 0.03096595168537221 0.2321096256794494 chr4 191154276 5561659 0.029095132561931285 0.226996691577177 chr5 180915260 4501976 0.024884445900251864 0.20381778510284523 chr6 171115067 4613240 0.026959870225805423 0.2392031390811128 chr7 159138663 4890647 0.03073198497338136 0.3366195157087023 chr8 146364022 7052287 0.04818320037693416 0.45595797872716287 chr9 141213431 3021317 0.021395394040103734 0.25798656058890623 chr10 135534747 4224635 0.0311701249569603 0.2661936646547021 chr11 135006516 3583165 0.02654068193271501 0.2689567921098826 chr12 133851895 4010981 0.029965814081302323 0.22705288536066215 chr13 115169878 2741639 0.02380517412721406 0.20400378925010454 chr14 107349540 2358791 0.021972995878696826 0.199050649758363 chr15 102531392 2016450 0.01966665974846026 0.1874350785224608 chr16 90354753 1927632 0.021334040944143803 0.21860796590500678 chr17 81195210 1831395 0.022555456165456067 0.20611638528819556 chr18 78077248 2059720 0.02638054046167201 0.48443548224381894 chr19 59128983 1240785 0.02098437918338626 0.2347425571023669 chr20 63025520 1764137 0.027990836093061987 0.22381929925381142 chr21 48129895 1016786 0.021125871976242626 0.19730791721759905 chr22 51304566 839117 0.016355600786097674 0.16304101054067466 chrMT 16571 79853 4.818840142417477 4.214315527678485 chrX 155270560 4552633 0.029320645201511477 0.23669248547243643 chrY 59373566 252209 0.004247833118192699 0.09365952076644284