BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10173891.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 = 4,377,240 number of mapped reads = 4,263,886 (97.41%) number of supplementary alignments = 459,742 (10.5%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 2,133,856 number of mapped paired reads (second in pair) = 2,130,030 number of mapped paired reads (both in pair) = 4,185,920 number of mapped paired reads (singletons) = 77,966 number of mapped bases = 504,330,324 bp number of sequenced bases = 504,034,377 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 3,477,136 duplication rate = 66.54% >>>>>>> Insert size mean insert size = 1,130,540.0582 std insert size = 10,216,734.0338 median insert size = 202 >>>>>>> Mapping quality mean mapping quality = 52.6783 >>>>>>> ACTG content number of A's = 150,816,037 bp (29.92%) number of C's = 99,389,298 bp (19.72%) number of T's = 150,559,380 bp (29.87%) number of G's = 103,263,154 bp (20.49%) number of N's = 6,508 bp (0%) GC percentage = 40.21% >>>>>>> Mismatches and indels general error rate = 0.0105 number of mismatches = 5,145,953 number of insertions = 51,023 mapped reads with insertion percentage = 1.16% number of deletions = 124,712 mapped reads with deletion percentage = 2.86% homopolymer indels = 42.15% >>>>>>> Coverage mean coverageData = 0.1629X std coverageData = 2.4393X There is a 3.03% of reference with a coverageData >= 1X There is a 2.46% of reference with a coverageData >= 2X There is a 1.98% of reference with a coverageData >= 3X There is a 1.68% of reference with a coverageData >= 4X There is a 1.34% of reference with a coverageData >= 5X There is a 1.11% of reference with a coverageData >= 6X There is a 0.86% of reference with a coverageData >= 7X There is a 0.71% of reference with a coverageData >= 8X There is a 0.54% of reference with a coverageData >= 9X There is a 0.45% of reference with a coverageData >= 10X There is a 0.34% of reference with a coverageData >= 11X There is a 0.29% of reference with a coverageData >= 12X There is a 0.22% of reference with a coverageData >= 13X There is a 0.19% of reference with a coverageData >= 14X There is a 0.14% of reference with a coverageData >= 15X There is a 0.13% of reference with a coverageData >= 16X There is a 0.1% of reference with a coverageData >= 17X There is a 0.09% of reference with a coverageData >= 18X There is a 0.07% of reference with a coverageData >= 19X There is a 0.06% of reference with a coverageData >= 20X There is a 0.04% of reference with a coverageData >= 21X There is a 0.04% of reference with a coverageData >= 22X There is a 0.03% of reference with a coverageData >= 23X There is a 0.03% of reference with a coverageData >= 24X There is a 0.02% of reference with a coverageData >= 25X There is a 0.02% of reference with a coverageData >= 26X There is a 0.02% of reference with a coverageData >= 27X There is a 0.02% 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 0.01% of reference with a coverageData >= 35X There is a 0.01% 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 44302910 0.17774443177816596 2.132718969589781 chr2 243199373 58619349 0.24103412881742914 7.039682585231177 chr3 198022430 29713715 0.15005226933130758 1.1965064317793646 chr4 191154276 31499259 0.16478448538603446 1.4168818164623274 chr5 180915260 33295345 0.1840383448029757 1.319452755577243 chr6 171115067 29751596 0.17386894398960204 1.321542419841394 chr7 159138663 32067230 0.2015049604884515 2.1129732062670596 chr8 146364022 21851586 0.14929615694764115 1.2919715825462565 chr9 141213431 20556604 0.14557116737713144 1.2773818631369633 chr10 135534747 19808756 0.14615260247617534 2.00950084704933 chr11 135006516 25632409 0.18986053236126765 1.3497504550589485 chr12 133851895 17653410 0.1318876359576381 1.1048231403803865 chr13 115169878 16478661 0.14308134458560423 1.1721745228646971 chr14 107349540 12121844 0.11291938465688814 1.0278637757977218 chr15 102531392 15046109 0.14674636427446533 1.1587545746514814 chr16 90354753 20511582 0.22701165482683572 1.9320148768211542 chr17 81195210 12355272 0.15216749855071499 1.2597054458457324 chr18 78077248 7580328 0.09708754079037211 1.5478815090074853 chr19 59128983 9762812 0.16511043323711486 1.8660763026157943 chr20 63025520 14953266 0.2372573205266692 1.489626926235807 chr21 48129895 7659695 0.15914630605364918 1.2354179242770342 chr22 51304566 4682706 0.09127269490984487 0.8847619324782775 chrMT 16571 1051615 63.461167099149115 51.71673417511057 chrX 155270560 16724855 0.10771426985257218 1.0041003438924172 chrY 59373566 649410 0.010937695741569574 0.5257415332974426