BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6236106.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 1,527,609 number of mapped reads = 1,328,645 (86.98%) number of supplementary alignments = 8,880 (0.58%) number of secondary alignments = 0 number of mapped bases = 86,827,220 bp number of sequenced bases = 86,780,667 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 72,114 duplication rate = 4.6% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.1097 >>>>>>> ACTG content number of A's = 23,387,609 bp (26.95%) number of C's = 15,555,064 bp (17.92%) number of T's = 28,047,880 bp (32.32%) number of G's = 19,743,160 bp (22.75%) number of N's = 46,954 bp (0.05%) GC percentage = 40.68% >>>>>>> Mismatches and indels general error rate = 0.0083 number of mismatches = 712,222 number of insertions = 6,173 mapped reads with insertion percentage = 0.46% number of deletions = 26,604 mapped reads with deletion percentage = 1.98% homopolymer indels = 46.57% >>>>>>> Coverage mean coverageData = 0.028X std coverageData = 0.2838X There is a 2.32% of reference with a coverageData >= 1X There is a 0.36% of reference with a coverageData >= 2X There is a 0.07% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% 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 12183422 0.04888020720317483 0.55587799895509 chr2 243199373 8957748 0.03683294035466119 0.3117374344685229 chr3 198022430 4832140 0.024401983149080635 0.18193614039423608 chr4 191154276 4409309 0.023066755775842544 0.18076696369484205 chr5 180915260 5452183 0.03013666729937541 0.2032217326109423 chr6 171115067 2959340 0.017294444328505566 0.1828939314698093 chr7 159138663 4640306 0.029158885166705215 0.3525768610496526 chr8 146364022 3530882 0.024123974947887126 0.43934724405963765 chr9 141213431 4088200 0.028950504006945346 0.2402511322434843 chr10 135534747 4205424 0.031028382706908362 0.23198581687542214 chr11 135006516 2562811 0.018982868945377422 0.18970179142521187 chr12 133851895 1435691 0.010725966935320564 0.12332197734102769 chr13 115169878 1993872 0.017312443449840245 0.1530086362286341 chr14 107349540 3446877 0.032108912623193354 0.2137869710278179 chr15 102531392 3323730 0.03241670609524154 0.21371775009817845 chr16 90354753 1273289 0.014092108690729308 0.14871586084278118 chr17 81195210 3470569 0.04274351898344742 0.2540524305204874 chr18 78077248 1687273 0.021610303170521584 0.3349911387249462 chr19 59128983 2840700 0.04804242954762134 0.36657333964099187 chr20 63025520 2033411 0.03226329588395304 0.21094712029899446 chr21 48129895 1555543 0.03231968405499326 0.21615391070348816 chr22 51304566 1620123 0.03157853435501238 0.20732021749426768 chrMT 16571 155990 9.413433106028604 6.438904828761718 chrX 155270560 3984957 0.025664601196775487 0.19507959186455692 chrY 59373566 183430 0.0030894219828399728 0.07858475635737025