BamQC report ----------------------------------- >>>>>>> Input bam file = SRR23117307.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP418207/SRP418207.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 = 6,953,048 number of mapped reads = 6,426,043 (92.42%) number of supplementary alignments = 75,765 (1.09%) number of secondary alignments = 0 number of mapped bases = 1,620,941,034 bp number of sequenced bases = 1,617,376,746 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 3,610,370 duplication rate = 34.78% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 52.0311 >>>>>>> ACTG content number of A's = 457,664,451 bp (28.3%) number of C's = 343,472,290 bp (21.24%) number of T's = 462,082,680 bp (28.57%) number of G's = 354,157,325 bp (21.9%) number of N's = 0 bp (0%) GC percentage = 43.13% >>>>>>> Mismatches and indels general error rate = 0.012 number of mismatches = 11,384,181 number of insertions = 6,936,273 mapped reads with insertion percentage = 48.32% number of deletions = 2,813,977 mapped reads with deletion percentage = 28.5% homopolymer indels = 30.92% >>>>>>> Coverage mean coverageData = 0.5236X std coverageData = 8.2671X There is a 12.56% of reference with a coverageData >= 1X There is a 7.55% of reference with a coverageData >= 2X There is a 5.4% of reference with a coverageData >= 3X There is a 4.16% of reference with a coverageData >= 4X There is a 3.33% of reference with a coverageData >= 5X There is a 2.72% of reference with a coverageData >= 6X There is a 2.26% of reference with a coverageData >= 7X There is a 1.9% of reference with a coverageData >= 8X There is a 1.6% of reference with a coverageData >= 9X There is a 1.36% of reference with a coverageData >= 10X There is a 1.15% of reference with a coverageData >= 11X There is a 0.98% of reference with a coverageData >= 12X There is a 0.84% of reference with a coverageData >= 13X There is a 0.72% of reference with a coverageData >= 14X There is a 0.62% of reference with a coverageData >= 15X There is a 0.53% of reference with a coverageData >= 16X There is a 0.46% of reference with a coverageData >= 17X There is a 0.39% of reference with a coverageData >= 18X There is a 0.34% of reference with a coverageData >= 19X There is a 0.29% of reference with a coverageData >= 20X There is a 0.25% of reference with a coverageData >= 21X There is a 0.22% of reference with a coverageData >= 22X There is a 0.19% of reference with a coverageData >= 23X There is a 0.16% of reference with a coverageData >= 24X There is a 0.14% of reference with a coverageData >= 25X There is a 0.12% of reference with a coverageData >= 26X There is a 0.11% of reference with a coverageData >= 27X There is a 0.09% of reference with a coverageData >= 28X There is a 0.08% of reference with a coverageData >= 29X There is a 0.07% of reference with a coverageData >= 30X There is a 0.06% of reference with a coverageData >= 31X There is a 0.06% of reference with a coverageData >= 32X There is a 0.05% of reference with a coverageData >= 33X There is a 0.04% of reference with a coverageData >= 34X There is a 0.04% of reference with a coverageData >= 35X There is a 0.03% of reference with a coverageData >= 36X There is a 0.03% of reference with a coverageData >= 37X There is a 0.03% of reference with a coverageData >= 38X There is a 0.02% of reference with a coverageData >= 39X There is a 0.02% of reference with a coverageData >= 40X There is a 0.02% of reference with a coverageData >= 41X There is a 0.02% of reference with a coverageData >= 42X There is a 0.02% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 168061545 0.6742673070411327 24.6790630046663 chr2 243199373 104723888 0.43060920226961275 4.128797539298512 chr3 198022430 97779612 0.49378048739226155 2.143298398379346 chr4 191154276 60951860 0.31886213207179315 3.408956818487964 chr5 180915260 108571869 0.6001255449650847 2.47495917718344 chr6 171115067 112641000 0.6582763398619947 2.671994068171467 chr7 159138663 97222437 0.6109290801318344 8.418353510357331 chr8 146364022 53215508 0.36358325818622284 1.7635022642696472 chr9 141213431 75613358 0.5354544356336757 2.785146675282856 chr10 135534747 78058803 0.5759320375608182 11.10789627185895 chr11 135006516 83334288 0.617261229080232 2.5743943470215838 chr12 133851895 81436764 0.608409496182329 2.560743134212124 chr13 115169878 44014063 0.3821664463341708 1.898984428272179 chr14 107349540 49098726 0.45737248617926074 2.1280145032558204 chr15 102531392 57956610 0.56525722385589 2.5119624638744202 chr16 90354753 38181409 0.4225722248391294 3.9421093568798606 chr17 81195210 50771195 0.6252979085835236 2.739510345235227 chr18 78077248 46801788 0.5994292729169962 3.920445279024895 chr19 59128983 29122707 0.4925284610425314 13.531668981049183 chr20 63025520 27302571 0.4331986630177744 3.0589314752983183 chr21 48129895 27534899 0.5720955551637916 3.689996765078777 chr22 51304566 18760632 0.36567178055847893 1.9920654660614856 chrMT 16571 215666 13.014664172349285 39.23407129190134 chrX 155270560 106357249 0.6849801340318474 2.8840504014502364 chrY 59373566 3212587 0.05410803521553682 2.6867422548619393