BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716894.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 = 4,489,145 number of mapped reads = 3,770,756 (84%) number of supplementary alignments = 76,052 (1.69%) number of secondary alignments = 0 number of mapped bases = 270,912,386 bp number of sequenced bases = 270,825,232 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 194,580 duplication rate = 3.74% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.8787 >>>>>>> ACTG content number of A's = 73,151,695 bp (27.01%) number of C's = 55,706,285 bp (20.57%) number of T's = 80,496,123 bp (29.72%) number of G's = 61,438,961 bp (22.69%) number of N's = 32,168 bp (0.01%) GC percentage = 43.25% >>>>>>> Mismatches and indels general error rate = 0.0071 number of mismatches = 1,884,195 number of insertions = 22,872 mapped reads with insertion percentage = 0.6% number of deletions = 51,550 mapped reads with deletion percentage = 1.35% homopolymer indels = 39.99% >>>>>>> Coverage mean coverageData = 0.0875X std coverageData = 0.6196X There is a 6.81% of reference with a coverageData >= 1X There is a 1.3% of reference with a coverageData >= 2X There is a 0.32% of reference with a coverageData >= 3X There is a 0.1% of reference with a coverageData >= 4X There is a 0.04% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% 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 21300853 0.08545957845376842 0.7730048171571187 chr2 243199373 23179311 0.09530991266165806 0.9196334449935006 chr3 198022430 18145415 0.09163312964091996 0.3731446075430391 chr4 191154276 17702006 0.09260585936356454 0.415358670948 chr5 180915260 16534451 0.09139334625503676 0.37847573814410246 chr6 171115067 15953191 0.0932307790289443 0.46698578591362266 chr7 159138663 14862381 0.09339264714068887 0.8394966186239586 chr8 146364022 13999263 0.09564688650056365 0.835435687044538 chr9 141213431 11405084 0.08076486718887242 0.667710596612299 chr10 135534747 12784758 0.09432826845502577 0.6111765526396223 chr11 135006516 12244904 0.0906986148727814 0.6325397124377439 chr12 133851895 12380021 0.09249044251484075 0.386141591094319 chr13 115169878 8667024 0.07525426049335573 0.3367258429825686 chr14 107349540 8243322 0.0767895419020892 0.45976807698578714 chr15 102531392 7679176 0.07489585238440925 0.3404471140873277 chr16 90354753 7833949 0.0867021240155457 0.4339597409866679 chr17 81195210 7246189 0.08924404530759882 0.4219111451393825 chr18 78077248 7420992 0.09504679263285509 1.2805622855875987 chr19 59128983 5171120 0.08745491191688516 0.709975959463906 chr20 63025520 5560842 0.08823159253584897 0.3928726376454825 chr21 48129895 3490263 0.07251756938177405 0.3726336673977465 chr22 51304566 2893455 0.05639761186168108 0.2940147755051717 chrMT 16571 4074 0.24585118580652948 0.7854203055466462 chrX 155270560 15541992 0.10009619338012306 0.541653905069932 chrY 59373566 668350 0.011256692919539311 0.2717694218765219