BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6240272.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 = 2,599,942 number of mapped reads = 2,107,119 (81.04%) number of supplementary alignments = 19,293 (0.74%) number of secondary alignments = 0 number of mapped bases = 134,082,590 bp number of sequenced bases = 134,025,973 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 290,706 duplication rate = 10.6% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.4879 >>>>>>> ACTG content number of A's = 37,416,317 bp (27.92%) number of C's = 23,956,607 bp (17.87%) number of T's = 43,150,636 bp (32.2%) number of G's = 29,468,443 bp (21.99%) number of N's = 33,970 bp (0.03%) GC percentage = 39.86% >>>>>>> Mismatches and indels general error rate = 0.0083 number of mismatches = 1,091,181 number of insertions = 9,364 mapped reads with insertion percentage = 0.44% number of deletions = 33,438 mapped reads with deletion percentage = 1.57% homopolymer indels = 46.87% >>>>>>> Coverage mean coverageData = 0.0433X std coverageData = 0.4425X There is a 2.38% of reference with a coverageData >= 1X There is a 1% of reference with a coverageData >= 2X There is a 0.46% of reference with a coverageData >= 3X There is a 0.21% of reference with a coverageData >= 4X There is a 0.1% of reference with a coverageData >= 5X There is a 0.05% of reference with a coverageData >= 6X There is a 0.03% of reference with a coverageData >= 7X There is a 0.02% 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% 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 10412812 0.04177647364818401 0.6300606796129672 chr2 243199373 10443696 0.04294293965963473 0.4746466703766268 chr3 198022430 8085463 0.04083104626076955 0.3363228236586859 chr4 191154276 13811516 0.072253241146434 0.4515833229470464 chr5 180915260 8942746 0.049430578714034404 0.36363814190592286 chr6 171115067 8618078 0.05036422654704042 0.40974891448013717 chr7 159138663 5736897 0.036049674490478786 0.4752065330207263 chr8 146364022 12676161 0.08660708298928817 0.6975477993305568 chr9 141213431 5272412 0.03733647686812453 0.3963931289273591 chr10 135534747 4842661 0.035730033125748926 0.4964118682926765 chr11 135006516 4872410 0.03609018397304616 0.37766080707584104 chr12 133851895 6059142 0.04526751003413138 0.3555075189706835 chr13 115169878 3619073 0.03142378079101551 0.29804513263823196 chr14 107349540 4664381 0.04345040509721793 0.3604666447750524 chr15 102531392 3772858 0.03679710112586787 0.3515093593390607 chr16 90354753 3054764 0.033808559025112934 0.3295851780048115 chr17 81195210 2495754 0.030737699920968243 0.3228458292610405 chr18 78077248 2525303 0.0323436476654505 0.633790994127112 chr19 59128983 1751422 0.029620364009981366 0.5260231415056762 chr20 63025520 2708718 0.042978114262286135 0.3404916061165638 chr21 48129895 1464512 0.030428323186659768 0.2950734679998898 chr22 51304566 971333 0.018932681352377096 0.22378911294963927 chrMT 16571 23324 1.4075191599782753 2.1674450583436173 chrX 155270560 6929539 0.04462880149334169 0.3670104612034666 chrY 59373566 327615 0.0055178595808107606 0.12362154713650293