BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10174038.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 = 1,666,154 number of mapped reads = 1,624,324 (97.49%) number of supplementary alignments = 159,729 (9.59%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 813,828 number of mapped paired reads (second in pair) = 810,496 number of mapped paired reads (both in pair) = 1,597,528 number of mapped paired reads (singletons) = 26,796 number of mapped bases = 192,233,907 bp number of sequenced bases = 192,123,903 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,200,659 duplication rate = 62.53% >>>>>>> Insert size mean insert size = 1,117,698.6862 std insert size = 9,917,797.0739 median insert size = 200 >>>>>>> Mapping quality mean mapping quality = 53.0649 >>>>>>> ACTG content number of A's = 58,062,274 bp (30.22%) number of C's = 37,429,955 bp (19.48%) number of T's = 57,920,672 bp (30.15%) number of G's = 38,708,839 bp (20.15%) number of N's = 2,163 bp (0%) GC percentage = 39.63% >>>>>>> Mismatches and indels general error rate = 0.0108 number of mismatches = 2,004,686 number of insertions = 21,876 mapped reads with insertion percentage = 1.29% number of deletions = 43,752 mapped reads with deletion percentage = 2.63% homopolymer indels = 42.46% >>>>>>> Coverage mean coverageData = 0.0621X std coverageData = 1.0343X There is a 1.5% of reference with a coverageData >= 1X There is a 1.13% of reference with a coverageData >= 2X There is a 0.83% of reference with a coverageData >= 3X There is a 0.65% of reference with a coverageData >= 4X There is a 0.47% of reference with a coverageData >= 5X There is a 0.37% of reference with a coverageData >= 6X There is a 0.26% of reference with a coverageData >= 7X There is a 0.21% of reference with a coverageData >= 8X There is a 0.15% of reference with a coverageData >= 9X There is a 0.12% of reference with a coverageData >= 10X There is a 0.09% of reference with a coverageData >= 11X There is a 0.07% of reference with a coverageData >= 12X There is a 0.05% of reference with a coverageData >= 13X There is a 0.05% of reference with a coverageData >= 14X There is a 0.03% of reference with a coverageData >= 15X There is a 0.03% of reference with a coverageData >= 16X There is a 0.02% of reference with a coverageData >= 17X There is a 0.02% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% 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 15306738 0.0614110325526531 0.8254903965077219 chr2 243199373 17344953 0.07131989193080691 2.638096499200078 chr3 198022430 12927372 0.06528236220512999 0.6901871789971548 chr4 191154276 13381728 0.07000485827478953 0.8602524401269158 chr5 180915260 11802155 0.06523581813938747 0.6946692595553418 chr6 171115067 11444976 0.06688467708106616 0.7410476707422966 chr7 159138663 10733614 0.06744818510885692 0.828255085858053 chr8 146364022 10105962 0.06904676341840346 0.8857170747459303 chr9 141213431 8304838 0.058810539062675984 0.7820902814128656 chr10 135534747 9734042 0.07181953126750588 0.9497929935809291 chr11 135006516 8593787 0.06365460908568295 0.6846841191098358 chr12 133851895 8781083 0.06560297857568621 0.6961938775804901 chr13 115169878 6627184 0.057542684902383935 0.6570876683679303 chr14 107349540 5955368 0.055476418436446025 0.6415645430593591 chr15 102531392 5519085 0.05382824608486735 0.616648625462033 chr16 90354753 5718559 0.06329007395991663 0.7653838925246954 chr17 81195210 5078136 0.06254231006976889 0.6943021476477775 chr18 78077248 5383389 0.06894952291351253 0.9337038384334091 chr19 59128983 3206017 0.05422073638574166 0.6746653588285428 chr20 63025520 3934559 0.06242802915390464 0.6729434809077397 chr21 48129895 2796150 0.05809590899793154 0.8204660651467299 chr22 51304566 2182660 0.042543191964629426 0.5862749118685407 chrMT 16571 357589 21.57920463460262 19.243691688461382 chrX 155270560 5417123 0.03488828146172719 0.5061926167791352 chrY 59373566 1596840 0.026894796920232146 0.5661840064367323