BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716878.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 = 411,108 number of mapped reads = 359,955 (87.56%) number of supplementary alignments = 940 (0.23%) number of secondary alignments = 0 number of mapped bases = 20,639,240 bp number of sequenced bases = 20,633,448 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 5,655 duplication rate = 1.21% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.9021 >>>>>>> ACTG content number of A's = 4,982,414 bp (24.15%) number of C's = 3,834,118 bp (18.58%) number of T's = 6,657,716 bp (32.27%) number of G's = 5,158,990 bp (25%) number of N's = 210 bp (0%) GC percentage = 43.59% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 102,106 number of insertions = 1,017 mapped reads with insertion percentage = 0.28% number of deletions = 3,616 mapped reads with deletion percentage = 1% homopolymer indels = 44.33% >>>>>>> Coverage mean coverageData = 0.0067X std coverageData = 0.0937X There is a 0.64% of reference with a coverageData >= 1X There is a 0.02% of reference with a coverageData >= 2X There is a 0% of reference with a coverageData >= 3X There is a 0% 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 2450829 0.009832789945185333 0.1273811217958341 chr2 243199373 2138797 0.008794418232320031 0.12071897404936323 chr3 198022430 1343054 0.006782332688271727 0.08493316016747263 chr4 191154276 891487 0.0046637042008937325 0.07095666710214439 chr5 180915260 1476758 0.008162705567236285 0.0924223429875972 chr6 171115067 796279 0.004653470988618436 0.07295833298623193 chr7 159138663 1106863 0.006955336805864707 0.10771989636184655 chr8 146364022 924552 0.006316798263442091 0.0852745289301263 chr9 141213431 566248 0.004009873536745949 0.07187663579149083 chr10 135534747 977787 0.007214290221827765 0.10645280832613573 chr11 135006516 890966 0.006599429615678698 0.09156577739735183 chr12 133851895 849697 0.0063480386288143325 0.08176364864986889 chr13 115169878 558084 0.004845746211522426 0.07119930284387632 chr14 107349540 442958 0.004126314840287159 0.0666949652458246 chr15 102531392 890620 0.008686315309168923 0.09590467755576253 chr16 90354753 634971 0.007027532906874307 0.08941185682070837 chr17 81195210 791975 0.009753962087172384 0.1031426396526547 chr18 78077248 683419 0.00875311332694513 0.12689813157983237 chr19 59128983 336299 0.005687549200702471 0.10090652831462567 chr20 63025520 540447 0.00857505023361965 0.09513375948129218 chr21 48129895 264991 0.005505746480435912 0.07719268803329932 chr22 51304566 246817 0.004810819372295246 0.07100271654919409 chrMT 16571 1164 0.07024319594472271 0.2555564308879626 chrX 155270560 787400 0.005071148065673235 0.0771337071817584 chrY 59373566 46778 7.878590280395151E-4 0.03115802097771141