BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524902.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 = 1,883,801 number of mapped reads = 1,711,326 (90.84%) number of supplementary alignments = 7,100 (0.38%) number of secondary alignments = 0 number of mapped bases = 98,445,617 bp number of sequenced bases = 98,411,897 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 69,373 duplication rate = 3.02% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.0949 >>>>>>> ACTG content number of A's = 25,877,108 bp (26.29%) number of C's = 17,745,109 bp (18.03%) number of T's = 30,802,458 bp (31.3%) number of G's = 23,985,087 bp (24.37%) number of N's = 2,135 bp (0%) GC percentage = 42.4% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 505,077 number of insertions = 7,920 mapped reads with insertion percentage = 0.46% number of deletions = 21,151 mapped reads with deletion percentage = 1.23% homopolymer indels = 43.54% >>>>>>> Coverage mean coverageData = 0.0318X std coverageData = 0.3046X There is a 2.86% of reference with a coverageData >= 1X There is a 0.23% of reference with a coverageData >= 2X There is a 0.03% 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 10721704 0.043015756418115406 0.5722978550681 chr2 243199373 8429992 0.034662885417883045 0.4162966128754489 chr3 198022430 8009610 0.040447993694451685 0.22200561045212353 chr4 191154276 5739111 0.030023450796360946 0.2007844226416155 chr5 180915260 4545071 0.025122651345165687 0.1740317412099784 chr6 171115067 5089494 0.029743108477992764 0.2214705039003154 chr7 159138663 5917084 0.037181938621666064 0.42919318345901636 chr8 146364022 4663950 0.03186541293597411 0.3079493948898774 chr9 141213431 3302883 0.023389297863600524 0.21195773660461822 chr10 135534747 5397144 0.03982110949009998 0.31540621959977494 chr11 135006516 4640035 0.03436897075397457 0.2454047498612921 chr12 133851895 4535335 0.033883233405100466 0.20445269090831808 chr13 115169878 3152270 0.02737061161078941 0.18257985783452937 chr14 107349540 3769768 0.035116759699203186 0.207943856215998 chr15 102531392 2734908 0.026673860040835103 0.18121375161752917 chr16 90354753 2622997 0.029029983624657796 0.20491109109966002 chr17 81195210 1962876 0.02417477582729326 0.17545172678280527 chr18 78077248 2131517 0.027300104122522352 0.4061953218430918 chr19 59128983 1753278 0.02965175301594482 0.42431235334951517 chr20 63025520 1819856 0.02887490654579288 0.18925965872451522 chr21 48129895 1283396 0.02666525659364102 0.18875429605326366 chr22 51304566 789824 0.015394809109193127 0.13380729101718822 chrMT 16571 2267 0.13680526220505704 0.38047691921168003 chrX 155270560 5146955 0.033148299329892286 0.2179881165326265 chrY 59373566 284292 0.0047881914318570655 0.1420674966941417