BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524835.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 1,402,571 number of mapped reads = 1,288,138 (91.84%) number of supplementary alignments = 9,113 (0.65%) number of secondary alignments = 0 number of mapped bases = 74,876,505 bp number of sequenced bases = 74,854,849 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 35,515 duplication rate = 1.86% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.5091 >>>>>>> ACTG content number of A's = 18,309,991 bp (24.46%) number of C's = 14,935,256 bp (19.95%) number of T's = 24,278,109 bp (32.43%) number of G's = 17,322,251 bp (23.14%) number of N's = 9,242 bp (0.01%) GC percentage = 43.09% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 363,456 number of insertions = 4,409 mapped reads with insertion percentage = 0.34% number of deletions = 13,854 mapped reads with deletion percentage = 1.07% homopolymer indels = 45.28% >>>>>>> Coverage mean coverageData = 0.0242X std coverageData = 0.2516X There is a 2.22% of reference with a coverageData >= 1X There is a 0.13% of reference with a coverageData >= 2X There is a 0.02% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0% 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 6364081 0.02553285915383938 0.4905739133110419 chr2 243199373 4897797 0.020139019848542127 0.24342653455553734 chr3 198022430 5378632 0.0271617311230854 0.17455856421645902 chr4 191154276 4069098 0.02128698392287076 0.16390562903167635 chr5 180915260 4242460 0.0234499842633507 0.16272005391676453 chr6 171115067 4852947 0.02836072290466391 0.19238304520901797 chr7 159138663 3460558 0.02174555155085097 0.35417997809267904 chr8 146364022 8097087 0.05532156666205852 0.33672101273206334 chr9 141213431 3131006 0.022172154431967593 0.21345747631629783 chr10 135534747 3737796 0.027578138320500205 0.2351401147465705 chr11 135006516 3631308 0.026897279535752185 0.22039633047720408 chr12 133851895 2962940 0.022135958553295042 0.16078827559167994 chr13 115169878 1977813 0.017173005948656124 0.1391767885099942 chr14 107349540 1591747 0.014827702102868816 0.1352289249129146 chr15 102531392 2234652 0.0217948079745177 0.15834934316066845 chr16 90354753 2153068 0.023829050808207068 0.1755937206455803 chr17 81195210 2124981 0.026171260595298663 0.19019289424397565 chr18 78077248 1785979 0.022874512687742272 0.34733157491468164 chr19 59128983 1152972 0.01949926992656038 0.3322863090985036 chr20 63025520 1592429 0.025266415889944265 0.16919066137506442 chr21 48129895 984076 0.020446252791534242 0.16046155389766958 chr22 51304566 468549 0.009132695908586381 0.10005815088597078 chrMT 16571 79498 4.797417174582101 3.413801368870662 chrX 155270560 3717173 0.023939972909223745 0.18844288230923043 chrY 59373566 187858 0.0031640006261372273 0.08861844872395698