BamQC report ----------------------------------- >>>>>>> Input bam file = SRR8751211.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP188831/SRP188831.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 = 5,043,555 number of mapped reads = 4,211,727 (83.51%) number of supplementary alignments = 237,643 (4.71%) number of secondary alignments = 0 number of mapped bases = 411,747,879 bp number of sequenced bases = 411,599,273 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 175,891 duplication rate = 2.04% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 50.8868 >>>>>>> ACTG content number of A's = 120,405,888 bp (29.25%) number of C's = 85,164,531 bp (20.69%) number of T's = 121,145,974 bp (29.43%) number of G's = 84,880,692 bp (20.62%) number of N's = 2,188 bp (0%) GC percentage = 41.31% >>>>>>> Mismatches and indels general error rate = 0.0056 number of mismatches = 1,781,499 number of insertions = 375,131 mapped reads with insertion percentage = 8.47% number of deletions = 67,746 mapped reads with deletion percentage = 1.57% homopolymer indels = 54.01% >>>>>>> Coverage mean coverageData = 0.133X std coverageData = 1.5116X There is a 10.28% of reference with a coverageData >= 1X There is a 1.95% of reference with a coverageData >= 2X There is a 0.44% of reference with a coverageData >= 3X There is a 0.12% of reference with a coverageData >= 4X There is a 0.04% of reference with a coverageData >= 5X There is a 0.02% 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 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% 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 0.01% 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 49038201 0.19674254292028423 4.035912030450496 chr2 243199373 30450539 0.1252081311903711 0.6764573173066156 chr3 198022430 26562041 0.13413652685708383 0.6031883165644704 chr4 191154276 19066087 0.09974188074139655 0.6422469595347527 chr5 180915260 32911214 0.18191508002144208 0.5106471916358069 chr6 171115067 22759726 0.1330083107176062 0.8699267710323936 chr7 159138663 22750192 0.1429582954332097 0.9479296199754806 chr8 146364022 20027173 0.13683125624957204 0.5454993918222655 chr9 141213431 17674243 0.12515978738594633 0.7489237047074447 chr10 135534747 21914653 0.16169029333857834 2.8275119980104115 chr11 135006516 18544126 0.13735726651889898 0.7411863510545024 chr12 133851895 21203053 0.15840681971667267 0.47570033001649065 chr13 115169878 11613429 0.10083738214952351 0.3765800117837387 chr14 107349540 8661933 0.08068905558421582 0.37178688523519815 chr15 102531392 10064280 0.0981580353458968 0.6199975701865869 chr16 90354753 12563009 0.13904093125018005 1.2560293772078703 chr17 81195210 11843674 0.14586665888295627 0.6867930680100744 chr18 78077248 8598643 0.11012994464149146 1.5245166296951311 chr19 59128983 8173951 0.13823933010990566 2.6931619766141353 chr20 63025520 7412126 0.11760515422958827 0.45554306356391167 chr21 48129895 5211393 0.10827767232818605 0.510354387162366 chr22 51304566 4870078 0.09492484548061472 0.3695524096279338 chrMT 16571 1480091 89.31814615895239 31.85754107083931 chrX 155270560 17226243 0.11094339454948833 0.4755135260645871 chrY 59373566 1127781 0.018994665066942418 0.81797474231067