BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6237253.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 = 3,137,148 number of mapped reads = 2,816,851 (89.79%) number of supplementary alignments = 33,195 (1.06%) number of secondary alignments = 0 number of mapped bases = 172,193,607 bp number of sequenced bases = 172,099,326 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 957,284 duplication rate = 22.27% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 39.4538 >>>>>>> ACTG content number of A's = 44,153,792 bp (25.66%) number of C's = 29,570,801 bp (17.18%) number of T's = 57,882,633 bp (33.63%) number of G's = 40,473,711 bp (23.52%) number of N's = 18,389 bp (0.01%) GC percentage = 40.7% >>>>>>> Mismatches and indels general error rate = 0.0066 number of mismatches = 1,090,428 number of insertions = 15,002 mapped reads with insertion percentage = 0.53% number of deletions = 52,899 mapped reads with deletion percentage = 1.85% homopolymer indels = 41.31% >>>>>>> Coverage mean coverageData = 0.0556X std coverageData = 0.8608X There is a 2.05% of reference with a coverageData >= 1X There is a 1.16% of reference with a coverageData >= 2X There is a 0.76% of reference with a coverageData >= 3X There is a 0.5% of reference with a coverageData >= 4X There is a 0.33% of reference with a coverageData >= 5X There is a 0.21% of reference with a coverageData >= 6X There is a 0.14% of reference with a coverageData >= 7X There is a 0.1% of reference with a coverageData >= 8X There is a 0.06% of reference with a coverageData >= 9X There is a 0.04% of reference with a coverageData >= 10X There is a 0.03% of reference with a coverageData >= 11X There is a 0.02% of reference with a coverageData >= 12X There is a 0.02% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% 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 12600884 0.0505550756481365 0.5256761665620763 chr2 243199373 12374217 0.050880957657732116 1.7710755593343082 chr3 198022430 6133946 0.030976016201800977 0.38390011853242656 chr4 191154276 14461324 0.07565263149017917 0.8986439137642996 chr5 180915260 22128407 0.12231365668103399 0.769347304226294 chr6 171115067 32800782 0.1916884502052645 1.2099608993055657 chr7 159138663 3121672 0.019616050186371116 0.3799607679682231 chr8 146364022 16030170 0.10952261205284451 0.7960241624025444 chr9 141213431 10251010 0.07259231595328917 0.7264486472782359 chr10 135534747 2610644 0.01926180597806406 1.0417020973418911 chr11 135006516 1905688 0.01411552609801441 0.29795459499020266 chr12 133851895 2624551 0.01960787331400874 0.36175270887525895 chr13 115169878 9012391 0.07825302202716582 0.6662793157332754 chr14 107349540 5466016 0.05091792661617367 0.5207684234641884 chr15 102531392 4872690 0.047523884197339286 0.5026626789224188 chr16 90354753 1252389 0.013860798224969969 0.4108014506034873 chr17 81195210 1597325 0.019672650640351813 0.33900257670612866 chr18 78077248 1443239 0.01848475755702865 2.025548189258324 chr19 59128983 1473649 0.024922617052283817 0.40135648082463193 chr20 63025520 937681 0.014877798707571156 0.3310118017603469 chr21 48129895 2284833 0.047472220747624735 0.6774882429403616 chr22 51304566 3371405 0.06571354682154411 0.5583376047773784 chrMT 16571 31257 1.886247058113572 3.0152133021327314 chrX 155270560 2717062 0.017498887103904306 0.3053301658943853 chrY 59373566 690375 0.011627649247141396 0.6787006460633066