BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524487.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 1,812,879 number of mapped reads = 1,672,637 (92.26%) number of supplementary alignments = 4,154 (0.23%) number of secondary alignments = 0 number of mapped bases = 97,721,956 bp number of sequenced bases = 97,691,980 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 96,577 duplication rate = 4.5% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.435 >>>>>>> ACTG content number of A's = 25,070,687 bp (25.66%) number of C's = 18,944,381 bp (19.39%) number of T's = 30,564,229 bp (31.29%) number of G's = 23,110,804 bp (23.66%) number of N's = 1,879 bp (0%) GC percentage = 43.05% >>>>>>> Mismatches and indels general error rate = 0.0048 number of mismatches = 455,476 number of insertions = 6,731 mapped reads with insertion percentage = 0.4% number of deletions = 17,230 mapped reads with deletion percentage = 1.02% homopolymer indels = 42.69% >>>>>>> Coverage mean coverageData = 0.0316X std coverageData = 0.3016X There is a 2.7% of reference with a coverageData >= 1X There is a 0.33% of reference with a coverageData >= 2X There is a 0.06% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0.01% 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 9496692 0.038100976286033005 0.5632660411385562 chr2 243199373 7448124 0.03062558882501724 0.3375856420569642 chr3 198022430 5400512 0.02727222365668374 0.18892751781266423 chr4 191154276 5703316 0.029836193672172943 0.2222660145417034 chr5 180915260 5433419 0.03003295023316441 0.19749287774541396 chr6 171115067 4230492 0.024723082976673236 0.23395234703748638 chr7 159138663 4903683 0.03081390095629998 0.39786533303156835 chr8 146364022 9223553 0.06301789793669375 0.33866748929160784 chr9 141213431 3947114 0.027951406406944393 0.25614916066677007 chr10 135534747 5086300 0.03752764595487827 0.3050829414972434 chr11 135006516 3458888 0.025620155993063328 0.27133674442728467 chr12 133851895 4605776 0.03440949416517413 0.2119341424769812 chr13 115169878 2111725 0.018335740531044063 0.1557555944273451 chr14 107349540 2398286 0.02234090616503806 0.17397880319339282 chr15 102531392 2541606 0.024788564267224616 0.18656584938297271 chr16 90354753 2983226 0.033016813183032 0.21808867738474763 chr17 81195210 3305212 0.040706982591707075 0.24510012247055737 chr18 78077248 2436249 0.031203059308647765 0.455876653413879 chr19 59128983 1931425 0.03266460713521827 0.3939615345559941 chr20 63025520 2771825 0.04397940707192896 0.2434735635921338 chr21 48129895 1334901 0.027735381512883 0.2033081707967878 chr22 51304566 733605 0.014299019701287406 0.1349338139878345 chrMT 16571 4927 0.2973266549996983 0.5783113372788102 chrX 155270560 5919264 0.03812225575794922 0.24827123635706078 chrY 59373566 311836 0.005252101583388136 0.15048458049467905