BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10173898.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP222840/SRP222840.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 = 4,093,786 number of mapped reads = 3,990,150 (97.47%) number of supplementary alignments = 444,060 (10.85%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 1,996,581 number of mapped paired reads (second in pair) = 1,993,569 number of mapped paired reads (both in pair) = 3,916,138 number of mapped paired reads (singletons) = 74,012 number of mapped bases = 472,886,349 bp number of sequenced bases = 472,620,625 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 3,142,349 duplication rate = 64.21% >>>>>>> Insert size mean insert size = 1,305,555.9965 std insert size = 10,642,386.7666 median insert size = 209 >>>>>>> Mapping quality mean mapping quality = 52.5609 >>>>>>> ACTG content number of A's = 141,906,229 bp (30.03%) number of C's = 92,555,826 bp (19.58%) number of T's = 141,906,482 bp (30.03%) number of G's = 96,246,948 bp (20.36%) number of N's = 5,140 bp (0%) GC percentage = 39.95% >>>>>>> Mismatches and indels general error rate = 0.0106 number of mismatches = 4,868,190 number of insertions = 53,097 mapped reads with insertion percentage = 1.28% number of deletions = 109,046 mapped reads with deletion percentage = 2.67% homopolymer indels = 42.75% >>>>>>> Coverage mean coverageData = 0.1528X std coverageData = 2.2958X There is a 3.25% of reference with a coverageData >= 1X There is a 2.51% of reference with a coverageData >= 2X There is a 1.94% of reference with a coverageData >= 3X There is a 1.59% of reference with a coverageData >= 4X There is a 1.22% of reference with a coverageData >= 5X There is a 0.98% of reference with a coverageData >= 6X There is a 0.73% of reference with a coverageData >= 7X There is a 0.59% of reference with a coverageData >= 8X There is a 0.44% of reference with a coverageData >= 9X There is a 0.36% of reference with a coverageData >= 10X There is a 0.26% of reference with a coverageData >= 11X There is a 0.22% of reference with a coverageData >= 12X There is a 0.16% of reference with a coverageData >= 13X There is a 0.14% of reference with a coverageData >= 14X There is a 0.11% of reference with a coverageData >= 15X There is a 0.09% of reference with a coverageData >= 16X There is a 0.07% of reference with a coverageData >= 17X There is a 0.06% of reference with a coverageData >= 18X There is a 0.05% of reference with a coverageData >= 19X There is a 0.04% of reference with a coverageData >= 20X There is a 0.03% of reference with a coverageData >= 21X There is a 0.03% of reference with a coverageData >= 22X There is a 0.02% of reference with a coverageData >= 23X There is a 0.02% of reference with a coverageData >= 24X There is a 0.02% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% 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 41574332 0.1667973055922697 1.8337190051914602 chr2 243199373 50862726 0.20914003754442245 6.615739848428774 chr3 198022430 35835953 0.18096916091778087 1.231709422359458 chr4 191154276 30777978 0.16101119286497154 1.459368540545883 chr5 180915260 28339576 0.15664558092003958 1.141071016556754 chr6 171115067 26191950 0.15306629894841464 1.1820345024438415 chr7 159138663 29931175 0.1880823580879274 1.8592205518054474 chr8 146364022 19674531 0.1344219073181796 1.1650278115470236 chr9 141213431 19457931 0.13779093718075586 1.2503849121094508 chr10 135534747 17232568 0.1271450191293012 2.1960610743672473 chr11 135006516 25206551 0.1867061809075941 1.258157902797219 chr12 133851895 18458557 0.1379028440351928 1.0659673290623317 chr13 115169878 15328621 0.13309574748355643 1.0541212407338592 chr14 107349540 11425534 0.10643300381166049 0.9457226105164417 chr15 102531392 15828480 0.15437691512078563 1.1210959255269592 chr16 90354753 18961256 0.20985344290631838 1.8173902941430458 chr17 81195210 11230596 0.13831599179311194 1.1373516735975449 chr18 78077248 8334350 0.10674492523097126 1.7045341674632004 chr19 59128983 8570662 0.14494857792497462 1.7264789076056273 chr20 63025520 11387822 0.18068588724059714 1.266931627176842 chr21 48129895 7154703 0.14865403300796728 1.172214924039464 chr22 51304566 4148882 0.08086769508975088 0.7698569619628226 chrMT 16571 1238939 74.76549393518798 58.77987721413825 chrX 155270560 14987956 0.09652799603479242 0.8981025747351788 chrY 59373566 744720 0.012542955563760479 0.6746237267525632