BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524900.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 = 1,141,201 number of mapped reads = 1,033,775 (90.59%) number of supplementary alignments = 3,189 (0.28%) number of secondary alignments = 0 number of mapped bases = 59,254,720 bp number of sequenced bases = 59,236,283 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 29,454 duplication rate = 2.04% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.6612 >>>>>>> ACTG content number of A's = 14,155,484 bp (23.9%) number of C's = 10,095,011 bp (17.04%) number of T's = 20,035,473 bp (33.82%) number of G's = 14,949,122 bp (25.24%) number of N's = 1,193 bp (0%) GC percentage = 42.28% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 305,462 number of insertions = 4,069 mapped reads with insertion percentage = 0.39% number of deletions = 11,874 mapped reads with deletion percentage = 1.14% homopolymer indels = 44.68% >>>>>>> Coverage mean coverageData = 0.0191X std coverageData = 0.207X There is a 1.78% of reference with a coverageData >= 1X There is a 0.1% 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 6573769 0.02637413288530984 0.36115661766656265 chr2 243199373 5145440 0.021157291388247124 0.267268049470313 chr3 198022430 4948469 0.024989436802689474 0.16915943980602335 chr4 191154276 3566228 0.018656281589013474 0.14878036289546395 chr5 180915260 2820885 0.015592299953027732 0.13222784926694295 chr6 171115067 3097833 0.018103800292466356 0.16028134371412206 chr7 159138663 3612428 0.022699876522149744 0.309939760404177 chr8 146364022 2901160 0.01982153783666863 0.20402675348349503 chr9 141213431 1988074 0.014078505039651646 0.1517972163882438 chr10 135534747 3260036 0.024053138196362296 0.23826057861794925 chr11 135006516 2824330 0.020919953226553895 0.17694749062009069 chr12 133851895 2812933 0.021015264669954802 0.15571091136503748 chr13 115169878 1981042 0.01720104279349849 0.14136641415255263 chr14 107349540 1778675 0.016569004394429637 0.13888666784860562 chr15 102531392 1673083 0.01631776344165892 0.13969021779990365 chr16 90354753 1625358 0.017988627560079767 0.15588873771640047 chr17 81195210 1201328 0.014795552594789766 0.13293855483410028 chr18 78077248 1332806 0.01707035063530928 0.2587970370703925 chr19 59128983 1041681 0.01761709650916878 0.25133523841299565 chr20 63025520 1093957 0.01735736571471366 0.1413599291331056 chr21 48129895 798210 0.016584494938125256 0.1403444863320222 chr22 51304566 457461 0.008916574793752276 0.09887273288076201 chrMT 16571 1142 0.06891557540281214 0.2741336563331981 chrX 155270560 2558020 0.016474597631386142 0.14670180345803427 chrY 59373566 160372 0.0027010673403042693 0.08430955421496254