BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6068173.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 = 3,645,710 number of mapped reads = 3,386,635 (92.89%) number of supplementary alignments = 30,591 (0.84%) number of secondary alignments = 0 number of mapped bases = 217,648,546 bp number of sequenced bases = 217,554,388 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 396,142 duplication rate = 9.9% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.2984 >>>>>>> ACTG content number of A's = 57,894,540 bp (26.61%) number of C's = 38,423,159 bp (17.66%) number of T's = 71,452,942 bp (32.84%) number of G's = 49,758,842 bp (22.87%) number of N's = 24,905 bp (0.01%) GC percentage = 40.53% >>>>>>> Mismatches and indels general error rate = 0.0059 number of mismatches = 1,262,705 number of insertions = 13,978 mapped reads with insertion percentage = 0.41% number of deletions = 54,518 mapped reads with deletion percentage = 1.59% homopolymer indels = 44.56% >>>>>>> Coverage mean coverageData = 0.0703X std coverageData = 0.7549X There is a 5.31% of reference with a coverageData >= 1X There is a 1.17% of reference with a coverageData >= 2X There is a 0.29% of reference with a coverageData >= 3X There is a 0.08% of reference with a coverageData >= 4X There is a 0.03% 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 0.01% 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 23706296 0.09511027858181344 1.6985999788219908 chr2 243199373 19459643 0.08001518572994018 1.0240450777957868 chr3 198022430 14111243 0.07126083141187592 0.3376828558830397 chr4 191154276 11402363 0.05965005459778467 0.3319111350686521 chr5 180915260 10347718 0.0571964907769527 0.30505059642096727 chr6 171115067 11713286 0.06845268628507155 0.4530043072775739 chr7 159138663 20668385 0.12987657813865133 1.0399155889943572 chr8 146364022 8417272 0.0575091602771069 1.0047743260674589 chr9 141213431 8113451 0.05745523596831239 0.5081913696753159 chr10 135534747 11102963 0.08191967923915482 0.5078771247444933 chr11 135006516 10319982 0.07644062157710965 0.46949618048478453 chr12 133851895 8460980 0.06321150701676656 0.3498776067476869 chr13 115169878 5087477 0.04417367707900151 0.29535148880664663 chr14 107349540 4677549 0.04357306980542255 0.3185810702789981 chr15 102531392 4253706 0.04148686482282422 0.2882078620009732 chr16 90354753 4604355 0.0509586363431263 0.31067462603961266 chr17 81195210 6025753 0.07421315863337258 0.36691379377740657 chr18 78077248 5696416 0.07295871903681851 0.9688001484889225 chr19 59128983 4502450 0.07614624455827357 1.0532971364361148 chr20 63025520 3220207 0.05109369982191341 0.3093380405858565 chr21 48129895 3839726 0.07977839968277513 0.3709650323519442 chr22 51304566 2207610 0.04302950345589124 0.254730664114431 chrMT 16571 375621 22.667370707863135 13.460454517986674 chrX 155270560 14754983 0.09502756349948116 0.466322270820684 chrY 59373566 579111 0.009753683987921494 0.32003431781009134