BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238241.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 = 1,243,082 number of mapped reads = 795,215 (63.97%) number of supplementary alignments = 8,639 (0.69%) number of secondary alignments = 0 number of mapped bases = 49,695,113 bp number of sequenced bases = 49,675,976 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 92,769 duplication rate = 8.36% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.1506 >>>>>>> ACTG content number of A's = 13,928,757 bp (28.04%) number of C's = 9,978,746 bp (20.09%) number of T's = 14,797,165 bp (29.79%) number of G's = 10,960,263 bp (22.06%) number of N's = 11,045 bp (0.02%) GC percentage = 42.15% >>>>>>> Mismatches and indels general error rate = 0.0088 number of mismatches = 432,031 number of insertions = 4,122 mapped reads with insertion percentage = 0.51% number of deletions = 11,895 mapped reads with deletion percentage = 1.48% homopolymer indels = 45.45% >>>>>>> Coverage mean coverageData = 0.0161X std coverageData = 0.303X There is a 0.96% of reference with a coverageData >= 1X There is a 0.34% of reference with a coverageData >= 2X There is a 0.14% of reference with a coverageData >= 3X There is a 0.06% of reference with a coverageData >= 4X There is a 0.03% 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% 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 3997997 0.016040068361554853 0.35279643264539257 chr2 243199373 3968413 0.01631752973310503 0.41844177906514596 chr3 198022430 3279718 0.016562356092691116 0.2198328156394907 chr4 191154276 3621470 0.018945273293284843 0.256166591766063 chr5 180915260 2831013 0.01564828196361103 0.21855704991727534 chr6 171115067 3033719 0.01772911674691978 0.29789613373332285 chr7 159138663 2461580 0.015468145537957674 0.24949269840799781 chr8 146364022 2305214 0.015749867819292367 0.2435700914006773 chr9 141213431 2124505 0.015044638353132288 0.2145413075609333 chr10 135534747 2020653 0.014908745135297297 0.22195551455202867 chr11 135006516 2231836 0.01653132060677723 0.2215453316425017 chr12 133851895 2203352 0.016461119209406783 0.22971766088652398 chr13 115169878 1753438 0.015224796886560912 0.2647818831786278 chr14 107349540 1529693 0.014249646528527277 0.5071042959906833 chr15 102531392 1776217 0.01732364074409523 0.6662757086625515 chr16 90354753 1420772 0.01572437478745584 0.2049579653977362 chr17 81195210 1470645 0.018112460082312737 0.23506550139065294 chr18 78077248 1303163 0.016690688175894725 0.2659501139855321 chr19 59128983 954998 0.016151098015671942 0.25554346746247425 chr20 63025520 1188505 0.018857519937955293 0.21963631572052714 chr21 48129895 589788 0.012254088649061046 0.1766981073044554 chr22 51304566 556854 0.010853887741687553 0.16435703332574586 chrMT 16571 6265 0.3780701225031682 1.1989411281555795 chrX 155270560 2919012 0.018799520012035765 0.300894272709356 chrY 59373566 146293 0.002463941613343554 0.07749051033246818