BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716895.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 = 943,704 number of mapped reads = 821,559 (87.06%) number of supplementary alignments = 18,844 (2%) number of secondary alignments = 0 number of mapped bases = 60,899,913 bp number of sequenced bases = 60,878,324 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 15,753 duplication rate = 1.28% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.9619 >>>>>>> ACTG content number of A's = 15,789,501 bp (25.94%) number of C's = 12,982,206 bp (21.32%) number of T's = 18,135,785 bp (29.79%) number of G's = 13,963,540 bp (22.94%) number of N's = 7,292 bp (0.01%) GC percentage = 44.26% >>>>>>> Mismatches and indels general error rate = 0.0077 number of mismatches = 459,696 number of insertions = 4,803 mapped reads with insertion percentage = 0.58% number of deletions = 12,517 mapped reads with deletion percentage = 1.5% homopolymer indels = 40.16% >>>>>>> Coverage mean coverageData = 0.0197X std coverageData = 0.1866X There is a 1.81% of reference with a coverageData >= 1X There is a 0.11% 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 4836434 0.01940389949921128 0.20832883324812307 chr2 243199373 5149325 0.021173265936010453 0.24598558591950628 chr3 198022430 4113147 0.0207711166861249 0.15268196617519683 chr4 191154276 3862683 0.020207149328953542 0.15656850712117437 chr5 180915260 3673823 0.020306871847073596 0.1514399310853141 chr6 171115067 3517857 0.02055842925859942 0.16591880317127972 chr7 159138663 3365964 0.021151139116959906 0.23339174460970316 chr8 146364022 3076726 0.021021053930862874 0.22127166440047166 chr9 141213431 2568748 0.01819053599795334 0.19546541776802254 chr10 135534747 2927271 0.02159793753848229 0.18972655617952014 chr11 135006516 2725810 0.020190210671016798 0.19044293227289083 chr12 133851895 2790433 0.020847168431944875 0.1545493358371251 chr13 115169878 1909305 0.01657816291165994 0.13599111938001102 chr14 107349540 1843786 0.01717553703537062 0.15272141602689676 chr15 102531392 1768573 0.01724908796712718 0.13924929694864777 chr16 90354753 1820259 0.02014569172692 0.16052655882823863 chr17 81195210 1668478 0.020548970807514385 0.15745377926572363 chr18 78077248 1658582 0.021242833763812988 0.3200267393610853 chr19 59128983 1240701 0.020982958560271533 0.1917820119231275 chr20 63025520 1283089 0.020358245358388156 0.15420046608275906 chr21 48129895 802291 0.01666928631363106 0.14271592343418119 chr22 51304566 694849 0.013543609354379881 0.12335884246297231 chrMT 16571 10824 0.6531893066199987 0.9054707144008147 chrX 155270560 3445742 0.022191856588911638 0.18175406690903315 chrY 59373566 145213 0.002445751700344224 0.07915048217399043