BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524994.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 = 2,995,191 number of mapped reads = 2,728,594 (91.1%) number of supplementary alignments = 11,761 (0.39%) number of secondary alignments = 0 number of mapped bases = 161,792,539 bp number of sequenced bases = 161,744,748 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 204,358 duplication rate = 5.64% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.9248 >>>>>>> ACTG content number of A's = 38,605,446 bp (23.87%) number of C's = 33,641,799 bp (20.8%) number of T's = 51,196,074 bp (31.65%) number of G's = 38,299,751 bp (23.68%) number of N's = 1,678 bp (0%) GC percentage = 44.48% >>>>>>> Mismatches and indels general error rate = 0.0049 number of mismatches = 782,734 number of insertions = 9,455 mapped reads with insertion percentage = 0.34% number of deletions = 28,758 mapped reads with deletion percentage = 1.05% homopolymer indels = 45.86% >>>>>>> Coverage mean coverageData = 0.0523X std coverageData = 0.4623X There is a 4.25% of reference with a coverageData >= 1X There is a 0.68% of reference with a coverageData >= 2X There is a 0.14% of reference with a coverageData >= 3X There is a 0.04% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% 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 17142068 0.06877442443764263 0.9899670773591291 chr2 243199373 15190084 0.0624593880017939 0.5217640043984366 chr3 198022430 8613741 0.043498814755479974 0.24462510043012478 chr4 191154276 9936029 0.05197910927192651 0.3194814833657227 chr5 180915260 6764171 0.0373886149791897 0.23995465279633016 chr6 171115067 10442026 0.06102341648266427 0.3947102738639123 chr7 159138663 9915454 0.06230700832267266 0.5230107942369401 chr8 146364022 10786536 0.0736966356390507 0.5538869083713754 chr9 141213431 4423245 0.031323118266278795 0.3243797320393259 chr10 135534747 8262335 0.06096100950407942 0.46064764124650254 chr11 135006516 6719200 0.04976944964641559 0.39109142131714425 chr12 133851895 8600859 0.06425653518017059 0.3053203808958519 chr13 115169878 4229542 0.036724376837492176 0.23020479373327066 chr14 107349540 3560940 0.033171450944270466 0.22362427326325163 chr15 102531392 4477221 0.04366683132518088 0.24606285942228412 chr16 90354753 4603920 0.05095382198654231 0.28546219932892725 chr17 81195210 4959897 0.061086078846276766 0.4645678947046505 chr18 78077248 3153467 0.04038906443013975 0.5709723862691981 chr19 59128983 4076273 0.06893866244917489 0.5320863856837148 chr20 63025520 4137703 0.06565123143767794 0.3105939747705858 chr21 48129895 2351649 0.048860463959042505 0.304143763539366 chr22 51304566 2357874 0.04595836557705215 0.25462625583128995 chrMT 16571 103585 6.250980628809366 4.563260581003689 chrX 155270560 6483680 0.041757304153472494 0.29767539796227993 chrY 59373566 501040 0.008438772230726381 0.24404954102896217