BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10174072.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 = 8,099,964 number of mapped reads = 7,915,658 (97.72%) number of supplementary alignments = 1,071,822 (13.23%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 3,962,178 number of mapped paired reads (second in pair) = 3,953,480 number of mapped paired reads (both in pair) = 7,795,140 number of mapped paired reads (singletons) = 120,518 number of mapped bases = 899,838,425 bp number of sequenced bases = 899,181,589 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 6,309,450 duplication rate = 64.59% >>>>>>> Insert size mean insert size = 1,386,746.1641 std insert size = 10,720,742.222 median insert size = 158 >>>>>>> Mapping quality mean mapping quality = 52.5716 >>>>>>> ACTG content number of A's = 267,016,555 bp (29.7%) number of C's = 179,733,655 bp (19.99%) number of T's = 265,142,132 bp (29.49%) number of G's = 187,282,455 bp (20.83%) number of N's = 6,792 bp (0%) GC percentage = 40.82% >>>>>>> Mismatches and indels general error rate = 0.0088 number of mismatches = 7,629,529 number of insertions = 95,381 mapped reads with insertion percentage = 1.16% number of deletions = 285,343 mapped reads with deletion percentage = 3.51% homopolymer indels = 40.45% >>>>>>> Coverage mean coverageData = 0.2907X std coverageData = 5.2488X There is a 6.33% of reference with a coverageData >= 1X There is a 4.75% of reference with a coverageData >= 2X There is a 3.53% of reference with a coverageData >= 3X There is a 2.82% of reference with a coverageData >= 4X There is a 2.11% of reference with a coverageData >= 5X There is a 1.73% of reference with a coverageData >= 6X There is a 1.29% of reference with a coverageData >= 7X There is a 1.11% of reference with a coverageData >= 8X There is a 0.83% of reference with a coverageData >= 9X There is a 0.74% of reference with a coverageData >= 10X There is a 0.55% of reference with a coverageData >= 11X There is a 0.5% of reference with a coverageData >= 12X There is a 0.37% of reference with a coverageData >= 13X There is a 0.34% of reference with a coverageData >= 14X There is a 0.25% of reference with a coverageData >= 15X There is a 0.23% of reference with a coverageData >= 16X There is a 0.17% of reference with a coverageData >= 17X There is a 0.16% of reference with a coverageData >= 18X There is a 0.12% of reference with a coverageData >= 19X There is a 0.11% of reference with a coverageData >= 20X There is a 0.08% of reference with a coverageData >= 21X There is a 0.08% of reference with a coverageData >= 22X There is a 0.06% of reference with a coverageData >= 23X There is a 0.05% of reference with a coverageData >= 24X There is a 0.04% of reference with a coverageData >= 25X There is a 0.04% of reference with a coverageData >= 26X There is a 0.03% of reference with a coverageData >= 27X There is a 0.03% of reference with a coverageData >= 28X There is a 0.02% of reference with a coverageData >= 29X There is a 0.02% of reference with a coverageData >= 30X There is a 0.02% 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 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% 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 72949968 0.29267717651945185 2.3801931375794245 chr2 243199373 78416849 0.32243853276710543 17.423951331953365 chr3 198022430 64979319 0.3281412060239843 1.7070092617307189 chr4 191154276 55296252 0.28927551691284165 2.108641727089548 chr5 180915260 59354324 0.3280780405146586 1.7093444178872192 chr6 171115067 57107318 0.3337363506394209 1.9694281474519817 chr7 159138663 49575277 0.3115225179439895 2.368887050039118 chr8 146364022 44071629 0.3011097153370109 2.5705454989481846 chr9 141213431 35068972 0.24834020214408642 1.9509464702042614 chr10 135534747 41829895 0.3086285688790934 2.6923662365375 chr11 135006516 41617044 0.30825952134043666 1.7068915161570097 chr12 133851895 40884994 0.30544949699815604 1.6981187078766595 chr13 115169878 31810415 0.2762042953627163 1.5737814019368628 chr14 107349540 27429257 0.2555135028990343 1.5182178674352262 chr15 102531392 26961511 0.2629585971094589 1.5675319822610976 chr16 90354753 27064015 0.2995306179410396 2.0128153333949204 chr17 81195210 25890062 0.3188619377916505 1.7867658132589228 chr18 78077248 26232212 0.33597767175400445 2.906312451045616 chr19 59128983 17941336 0.30342710274587337 1.9603178445519152 chr20 63025520 19872789 0.3153133682990636 1.7255843643852973 chr21 48129895 13078537 0.27173416854535004 1.9160093932007052 chr22 51304566 11622220 0.22653383326544463 1.6984284324468661 chrMT 16571 927873 55.99378432200833 40.67171072601821 chrX 155270560 22978201 0.14798813760960222 1.1471241569078938 chrY 59373566 6878156 0.1158454252183539 1.64580509896659