BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6237246.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 = 2,851,835 number of mapped reads = 2,603,185 (91.28%) number of supplementary alignments = 22,765 (0.8%) number of secondary alignments = 0 number of mapped bases = 178,719,862 bp number of sequenced bases = 178,650,437 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 133,613 duplication rate = 3.47% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.7559 >>>>>>> ACTG content number of A's = 50,994,498 bp (28.54%) number of C's = 33,065,425 bp (18.51%) number of T's = 56,592,344 bp (31.68%) number of G's = 37,995,146 bp (21.27%) number of N's = 3,024 bp (0%) GC percentage = 39.78% >>>>>>> Mismatches and indels general error rate = 0.0079 number of mismatches = 1,386,856 number of insertions = 15,534 mapped reads with insertion percentage = 0.59% number of deletions = 41,971 mapped reads with deletion percentage = 1.59% homopolymer indels = 47.71% >>>>>>> Coverage mean coverageData = 0.0577X std coverageData = 0.673X There is a 4.71% of reference with a coverageData >= 1X There is a 0.73% of reference with a coverageData >= 2X There is a 0.13% of reference with a coverageData >= 3X There is a 0.03% 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 0.01% 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 17452445 0.07001966506635103 1.0282924581468784 chr2 243199373 11610240 0.04773959676285843 0.5569946345366169 chr3 198022430 14491508 0.07318114417644506 0.313973445489992 chr4 191154276 9494346 0.0496684991760268 0.3534983208602456 chr5 180915260 10170377 0.05621624731932508 0.27796049592145944 chr6 171115067 20751662 0.12127314305992704 0.7692901864450504 chr7 159138663 11493160 0.07222104159565548 0.9945369109396422 chr8 146364022 10290899 0.07031030480974347 1.6908081027152697 chr9 141213431 8791493 0.062256776411019996 0.5667182880851125 chr10 135534747 6113903 0.0451094876799379 0.5498943118051914 chr11 135006516 7018926 0.051989535082884446 0.45226204773597806 chr12 133851895 6615084 0.04942092153420764 0.28115981832521614 chr13 115169878 5324420 0.04623101189705176 0.2512260873167418 chr14 107349540 4840139 0.045087654777095455 0.3021703606184174 chr15 102531392 4037549 0.03937866170782115 0.22797147654638109 chr16 90354753 4138984 0.04580814912968662 0.32725901746470676 chr17 81195210 4070392 0.05013093752697973 0.34458572649084723 chr18 78077248 4185099 0.05360203013302928 1.139148122021293 chr19 59128983 1866158 0.031560799887256644 0.6633704889280729 chr20 63025520 3640141 0.057756619858114616 0.2973322283539908 chr21 48129895 2532002 0.05260767761907646 0.34807282132516015 chr22 51304566 2208051 0.043038099182049414 0.23586310378008743 chrMT 16571 128878 7.777321827288636 5.6544106010826996 chrX 155270560 6973928 0.04491468311829364 0.30071892649754206 chrY 59373566 480078 0.008085719493419007 0.26447195804277235