BamQC report ----------------------------------- >>>>>>> Input bam file = ERR9714226.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/ERP137498/ERP137498.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 = 186,326 number of mapped reads = 28,513 (15.3%) number of supplementary alignments = 973 (0.52%) number of secondary alignments = 0 number of mapped bases = 3,268,830 bp number of sequenced bases = 3,205,896 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 22,650 duplication rate = 37.86% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 41.614 >>>>>>> ACTG content number of A's = 693,837 bp (21.64%) number of C's = 483,130 bp (15.07%) number of T's = 636,100 bp (19.84%) number of G's = 1,392,723 bp (43.44%) number of N's = 106 bp (0%) GC percentage = 58.51% >>>>>>> Mismatches and indels general error rate = 0.0432 number of mismatches = 126,075 number of insertions = 3,994 mapped reads with insertion percentage = 12.31% number of deletions = 9,839 mapped reads with deletion percentage = 31.87% homopolymer indels = 32.13% >>>>>>> Coverage mean coverageData = 0.0011X std coverageData = 1.1992X There is a 0.01% of reference with a coverageData >= 1X There is a 0.01% of reference with a coverageData >= 2X There is a 0% 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 401539 0.001610984953172895 1.2230142218207571 chr2 243199373 1025711 0.004217572551060812 3.817270035205663 chr3 198022430 90484 4.5693813574553146E-4 0.1479494732693708 chr4 191154276 58399 3.055071600909414E-4 0.08702326834789634 chr5 180915260 371691 0.0020545033072389804 1.5510403316094474 chr6 171115067 75684 4.422988654762938E-4 0.09296531804969575 chr7 159138663 62469 3.9254445665413187E-4 0.15000312008645986 chr8 146364022 71844 4.908583340241907E-4 0.13465057943355832 chr9 141213431 68726 4.866817519645139E-4 0.15991377073051424 chr10 135534747 116796 8.61742118425174E-4 0.5362425221242955 chr11 135006516 55509 4.111579325548998E-4 0.1410076779477789 chr12 133851895 70234 5.247142746839707E-4 0.1096108285695115 chr13 115169878 31541 2.7386501182192797E-4 0.06659875178513665 chr14 107349540 33379 3.109375224150937E-4 0.0736620509561947 chr15 102531392 39274 3.830436633494647E-4 0.06080373826423821 chr16 90354753 28174 3.1181536183270844E-4 0.10000619203610932 chr17 81195210 33120 4.0790583582455173E-4 0.08040948092197793 chr18 78077248 64748 8.292812779466817E-4 0.3679050522618837 chr19 59128983 16360 2.7668326377269163E-4 0.04450768969007305 chr20 63025520 32251 5.117133504015516E-4 0.08955625798872308 chr21 48129895 18701 3.8855268643324484E-4 0.13249971718052353 chr22 51304566 8072 1.5733492414690732E-4 0.03799333466373007 chrMT 16571 16198 0.977490797175789 4.481036276881819 chrX 155270560 474314 0.003054758094515792 0.3981086244081344 chrY 59373566 3612 6.083515347553826E-5 0.014480531169792137