BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10525188.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 = 2,957,159 number of mapped reads = 2,717,324 (91.89%) number of supplementary alignments = 8,606 (0.29%) number of secondary alignments = 0 number of mapped bases = 157,556,437 bp number of sequenced bases = 157,504,520 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 139,958 duplication rate = 3.75% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.7394 >>>>>>> ACTG content number of A's = 40,022,207 bp (25.41%) number of C's = 30,283,036 bp (19.23%) number of T's = 49,765,643 bp (31.6%) number of G's = 37,429,839 bp (23.76%) number of N's = 3,795 bp (0%) GC percentage = 42.99% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 806,894 number of insertions = 11,255 mapped reads with insertion percentage = 0.41% number of deletions = 32,602 mapped reads with deletion percentage = 1.19% homopolymer indels = 43.54% >>>>>>> Coverage mean coverageData = 0.0509X std coverageData = 0.458X There is a 4.38% of reference with a coverageData >= 1X There is a 0.51% of reference with a coverageData >= 2X There is a 0.08% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% 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 16785615 0.06734432569377631 0.8757292501510328 chr2 243199373 13253834 0.054497813199543076 0.672061009506362 chr3 198022430 13957969 0.07048680798432784 0.3072241161437749 chr4 191154276 8951224 0.04682722347262585 0.27074793621981696 chr5 180915260 7114422 0.03932460976481476 0.22775547852049188 chr6 171115067 7815641 0.04567476807872214 0.296928643514952 chr7 159138663 9218165 0.057925364120974175 0.6809490433637888 chr8 146364022 7284182 0.049767571978856937 0.3757757333360534 chr9 141213431 5270983 0.03732635743408855 0.3164349964729521 chr10 135534747 8599194 0.0634464164381404 0.49196139206594974 chr11 135006516 7201770 0.05334386971366627 0.3857106653542706 chr12 133851895 7155374 0.05345739782018028 0.2694120329626306 chr13 115169878 4907656 0.04261232264221032 0.24148161106347663 chr14 107349540 7214609 0.06720670624205749 0.3059096301038239 chr15 102531392 4390061 0.04281675021051114 0.24348807477027817 chr16 90354753 4269433 0.0472518916630761 0.2911051902191326 chr17 81195210 3156206 0.03887182507441018 0.2382199873169467 chr18 78077248 3313722 0.042441582982023135 0.6972417600522636 chr19 59128983 2894318 0.04894922681149446 0.5945116753649816 chr20 63025520 2917617 0.04629262876371349 0.2548389114621004 chr21 48129895 2048386 0.0425595360222581 0.25691250438022867 chr22 51304566 1291768 0.025178421741253985 0.18067670451599946 chrMT 16571 8101 0.4888660913644318 0.769752425992226 chrX 155270560 8057021 0.051890203783640634 0.2987652337334543 chrY 59373566 479166 0.008070359122441795 0.2209266867324238