BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10173895.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 = 3,126,332 number of mapped reads = 3,045,937 (97.43%) number of supplementary alignments = 342,442 (10.95%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 1,523,609 number of mapped paired reads (second in pair) = 1,522,328 number of mapped paired reads (both in pair) = 2,990,018 number of mapped paired reads (singletons) = 55,919 number of mapped bases = 360,781,963 bp number of sequenced bases = 360,574,283 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,441,483 duplication rate = 65.13% >>>>>>> Insert size mean insert size = 1,197,026.945 std insert size = 10,308,016.2101 median insert size = 208 >>>>>>> Mapping quality mean mapping quality = 52.6134 >>>>>>> ACTG content number of A's = 107,842,545 bp (29.91%) number of C's = 71,112,555 bp (19.72%) number of T's = 107,775,953 bp (29.89%) number of G's = 73,839,006 bp (20.48%) number of N's = 4,224 bp (0%) GC percentage = 40.2% >>>>>>> Mismatches and indels general error rate = 0.0105 number of mismatches = 3,703,887 number of insertions = 37,609 mapped reads with insertion percentage = 1.19% number of deletions = 82,784 mapped reads with deletion percentage = 2.65% homopolymer indels = 43.17% >>>>>>> Coverage mean coverageData = 0.1165X std coverageData = 1.8069X There is a 2.35% of reference with a coverageData >= 1X There is a 1.86% of reference with a coverageData >= 2X There is a 1.46% of reference with a coverageData >= 3X There is a 1.21% of reference with a coverageData >= 4X There is a 0.94% of reference with a coverageData >= 5X There is a 0.77% of reference with a coverageData >= 6X There is a 0.58% of reference with a coverageData >= 7X There is a 0.47% of reference with a coverageData >= 8X There is a 0.35% of reference with a coverageData >= 9X There is a 0.29% of reference with a coverageData >= 10X There is a 0.22% of reference with a coverageData >= 11X There is a 0.18% of reference with a coverageData >= 12X There is a 0.14% of reference with a coverageData >= 13X There is a 0.12% of reference with a coverageData >= 14X There is a 0.09% of reference with a coverageData >= 15X There is a 0.08% of reference with a coverageData >= 16X There is a 0.06% of reference with a coverageData >= 17X There is a 0.05% of reference with a coverageData >= 18X There is a 0.04% 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 0.02% 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 0.01% 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% 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 32222169 0.1292761834282451 1.5013459514716192 chr2 243199373 36710511 0.15094821399889052 4.95625526678249 chr3 198022430 28878162 0.14583278268022465 1.136581377153203 chr4 191154276 19185782 0.10036805035949078 1.0263369132586364 chr5 180915260 23724042 0.13113344888651185 1.0825541541299364 chr6 171115067 20776427 0.12141787023348447 1.0588012029867104 chr7 159138663 23900532 0.15018683423273452 1.8578164315613992 chr8 146364022 15164052 0.10360505124681528 1.0579962668230762 chr9 141213431 12050937 0.08533846189177288 0.9733514402650347 chr10 135534747 17552659 0.12950670871138306 1.7950730465176266 chr11 135006516 16529531 0.12243506083810059 1.0347228763532208 chr12 133851895 11848583 0.08852009902437318 0.8721710683172695 chr13 115169878 9838556 0.08542646888972132 0.8658483181005195 chr14 107349540 11662603 0.10864138775070671 0.9797553528462756 chr15 102531392 11367539 0.11086886443519658 0.9575454018974126 chr16 90354753 14691151 0.16259411389238151 1.4347334738442767 chr17 81195210 8970975 0.11048650530000477 1.0088223053980134 chr18 78077248 5612145 0.07187939052360043 1.1430111149670088 chr19 59128983 7409817 0.12531615840576862 1.5152395175602704 chr20 63025520 11122172 0.17647092796695688 1.229086181839662 chr21 48129895 5142746 0.10685138623302627 0.9893334824336895 chr22 51304566 3897179 0.07596164052922696 0.7763046404590095 chrMT 16571 1012074 61.07501056061795 54.391019408829706 chrX 155270560 11078824 0.07135173596334038 0.7876354408776957 chrY 59373566 432795 0.007289354996801101 0.35711877442589135