BamQC report ----------------------------------- >>>>>>> Input bam file = ERR9714254.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/ERP137498/ERP137498.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 = 415,470 number of mapped reads = 64,547 (15.54%) number of supplementary alignments = 1,041 (0.25%) number of secondary alignments = 0 number of mapped bases = 6,375,288 bp number of sequenced bases = 6,361,534 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 63,352 duplication rate = 35.15% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 9.7996 >>>>>>> ACTG content number of A's = 174,863 bp (2.75%) number of C's = 79,391 bp (1.25%) number of T's = 102,189 bp (1.61%) number of G's = 6,004,950 bp (94.39%) number of N's = 141 bp (0%) GC percentage = 95.64% >>>>>>> Mismatches and indels general error rate = 0.0315 number of mismatches = 154,721 number of insertions = 6,597 mapped reads with insertion percentage = 7.21% number of deletions = 3,136 mapped reads with deletion percentage = 4.67% homopolymer indels = 61.13% >>>>>>> Coverage mean coverageData = 0.0021X std coverageData = 7.7482X There is a 0% of reference with a coverageData >= 1X There is a 0% 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 82443 3.307634687899133E-4 0.7469095412170176 chr2 243199373 5995249 0.024651580824593657 27.62208355042796 chr3 198022430 7049 3.5596977574712114E-5 0.022192876026091605 chr4 191154276 4185 2.1893310929649305E-5 0.007391264240999348 chr5 180915260 4536 2.5072511848917553E-5 0.008447410735397166 chr6 171115067 10412 6.0847943916008285E-5 0.02648365495528566 chr7 159138663 12612 7.925163981049658E-5 0.08083094527202633 chr8 146364022 7584 5.1816012544394275E-5 0.02114591117623829 chr9 141213431 4270 3.023791695847968E-5 0.012666937188568464 chr10 135534747 71388 5.267136404511826E-4 1.0524576905307745 chr11 135006516 6527 4.834581465682738E-5 0.02840975658621745 chr12 133851895 7515 5.6144143495316225E-5 0.0443274444906159 chr13 115169878 1606 1.3944618401002387E-5 0.005320321230244455 chr14 107349540 8295 7.727094126346513E-5 0.08916629933130665 chr15 102531392 4692 4.576159465385977E-5 0.020241212383980526 chr16 90354753 2542 2.813355042871956E-5 0.008178021120117288 chr17 81195210 9104 1.1212484086191784E-4 0.08034270089685185 chr18 78077248 1262 1.6163479532475324E-5 0.005020512441583091 chr19 59128983 1976 3.341846755591924E-5 0.011523598399500411 chr20 63025520 4174 6.622714100573862E-5 0.020265398946537658 chr21 48129895 843 1.7515101580836608E-5 0.005163014824722781 chr22 51304566 1211 2.3604136910543205E-5 0.00806246883409532 chrMT 16571 2100 0.12672741536419047 0.6889026701839545 chrX 155270560 122658 7.899630168140051E-4 0.12395823545815424 chrY 59373566 1055 1.776885019841995E-5 0.008176039049594965