BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10525234.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 = 434,311 number of mapped reads = 411,629 (94.78%) number of supplementary alignments = 1,650 (0.38%) number of secondary alignments = 0 number of mapped bases = 26,021,127 bp number of sequenced bases = 26,011,842 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 6,254 duplication rate = 1.15% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.9328 >>>>>>> ACTG content number of A's = 7,039,179 bp (27.06%) number of C's = 5,100,141 bp (19.61%) number of T's = 7,579,427 bp (29.14%) number of G's = 6,292,417 bp (24.19%) number of N's = 678 bp (0%) GC percentage = 43.8% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 126,440 number of insertions = 1,600 mapped reads with insertion percentage = 0.39% number of deletions = 5,601 mapped reads with deletion percentage = 1.35% homopolymer indels = 43.56% >>>>>>> Coverage mean coverageData = 0.0084X std coverageData = 0.112X There is a 0.8% of reference with a coverageData >= 1X There is a 0.03% 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 2096916 0.008412881747644672 0.1707599370597794 chr2 243199373 2214799 0.009106927261691584 0.11676648265128753 chr3 198022430 1704621 0.008608221805984301 0.09562168453132534 chr4 191154276 1675297 0.008764109467266116 0.1005795884661445 chr5 180915260 1546264 0.008546896486233389 0.09505652040531097 chr6 171115067 1504515 0.00879241685946919 0.09953644085731408 chr7 159138663 1439506 0.009045608231608682 0.1405494871101922 chr8 146364022 1329772 0.009085374819776407 0.10912915131071575 chr9 141213431 1083379 0.007671926050716805 0.10034266394583927 chr10 135534747 1271598 0.00938208118690036 0.12008490464398533 chr11 135006516 1197120 0.008867127568864899 0.10473019602868162 chr12 133851895 1174435 0.008774138012764034 0.09627146265186044 chr13 115169878 811979 0.007050272294288616 0.08600462559095681 chr14 107349540 794650 0.007402453704040092 0.0904146385229781 chr15 102531392 734508 0.0071637377165424615 0.0870236866791688 chr16 90354753 772713 0.008551990618578748 0.09837453800181797 chr17 81195210 704690 0.008678960249009764 0.0975351323230447 chr18 78077248 691024 0.00885051686247958 0.15280145889164531 chr19 59128983 525524 0.008887756449320293 0.1352633106692314 chr20 63025520 553132 0.00877631791058606 0.09711367126033378 chr21 48129895 347620 0.007222538091969658 0.09070586684625795 chr22 51304566 312701 0.006094993572306995 0.08043469055275666 chrMT 16571 4954 0.29895600748295215 0.5961360475008141 chrX 155270560 1443302 0.009295400235563007 0.10168508983171552 chrY 59373566 86108 0.0014502750264317962 0.05720728802582102