BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524731.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 = 1,873,804 number of mapped reads = 1,693,963 (90.4%) number of supplementary alignments = 5,961 (0.32%) number of secondary alignments = 0 number of mapped bases = 96,125,708 bp number of sequenced bases = 96,094,239 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 73,108 duplication rate = 3.25% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.3884 >>>>>>> ACTG content number of A's = 23,841,070 bp (24.81%) number of C's = 15,895,280 bp (16.54%) number of T's = 31,367,199 bp (32.64%) number of G's = 24,979,316 bp (25.99%) number of N's = 11,374 bp (0.01%) GC percentage = 42.54% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 498,400 number of insertions = 6,877 mapped reads with insertion percentage = 0.4% number of deletions = 19,362 mapped reads with deletion percentage = 1.13% homopolymer indels = 42.84% >>>>>>> Coverage mean coverageData = 0.0311X std coverageData = 0.2717X There is a 2.74% of reference with a coverageData >= 1X There is a 0.26% 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 0.01% 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 7721749 0.030979858621896873 0.37977971773962715 chr2 243199373 8107735 0.03333781210036261 0.4274381430011301 chr3 198022430 6305697 0.03184334724101709 0.20244072334877694 chr4 191154276 6265026 0.032774710203186876 0.2381323077033492 chr5 180915260 5718205 0.03160709052403871 0.1981594406470294 chr6 171115067 5405597 0.03159042096509245 0.2163930576992049 chr7 159138663 5259372 0.03304898948409539 0.3306563544826181 chr8 146364022 4766146 0.03256364463665804 0.24452906546999745 chr9 141213431 4090290 0.028965304298852423 0.23928931061679662 chr10 135534747 4752666 0.03506603365703704 0.34156007669975597 chr11 135006516 4344872 0.03218268368617112 0.23467362834902325 chr12 133851895 4332511 0.03236794667718376 0.2032384028224342 chr13 115169878 2948638 0.025602510406410258 0.1769793100419866 chr14 107349540 2873317 0.026765992662846995 0.1879677924343447 chr15 102531392 2770651 0.027022465470867695 0.18535027409602375 chr16 90354753 2892881 0.032016921124226855 0.2259005295781424 chr17 81195210 2695744 0.03320077625268781 0.21217536067987916 chr18 78077248 2535333 0.032472110185031114 0.364102086508686 chr19 59128983 2096304 0.035453070451084874 0.31019049977547364 chr20 63025520 2056927 0.03263641458253736 0.21297017710692734 chr21 48129895 1280656 0.026608327319226438 0.20412138561995483 chr22 51304566 1197801 0.023346869360516567 0.17027648469532752 chrMT 16571 17643 1.0646913282240058 1.1872700688600004 chrX 155270560 5366932 0.03456503280467334 0.22505779650045346 chrY 59373566 323015 0.005440384025443242 0.15670656042213874