BamQC report ----------------------------------- >>>>>>> Input bam file = SRR8751219.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP188831/SRP188831.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 = 4,983,503 number of mapped reads = 2,932,673 (58.85%) number of supplementary alignments = 165,187 (3.31%) number of secondary alignments = 0 number of mapped bases = 288,318,075 bp number of sequenced bases = 288,221,371 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 108,556 duplication rate = 1.81% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 50.9665 >>>>>>> ACTG content number of A's = 85,101,209 bp (29.53%) number of C's = 58,960,296 bp (20.46%) number of T's = 85,668,422 bp (29.72%) number of G's = 58,489,339 bp (20.29%) number of N's = 2,105 bp (0%) GC percentage = 40.75% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 1,162,398 number of insertions = 230,223 mapped reads with insertion percentage = 7.49% number of deletions = 44,273 mapped reads with deletion percentage = 1.48% homopolymer indels = 53.52% >>>>>>> Coverage mean coverageData = 0.0931X std coverageData = 1.1307X There is a 7.52% of reference with a coverageData >= 1X There is a 1.17% of reference with a coverageData >= 2X There is a 0.24% of reference with a coverageData >= 3X There is a 0.07% 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 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% 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 32174219 0.12908380677615242 3.093043042917492 chr2 243199373 22666883 0.09320288420315952 0.5165931879216701 chr3 198022430 20187046 0.10194322936043154 0.46051178757755445 chr4 191154276 9303629 0.048670786731446175 0.3759163823648499 chr5 180915260 21418526 0.11838982515902749 0.4574537362213466 chr6 171115067 16917866 0.09886835973362883 0.8051670721926161 chr7 159138663 16789724 0.1055037392138955 0.7454842638004038 chr8 146364022 15114485 0.10326639561736012 0.48007794843117035 chr9 141213431 13101280 0.09277644418964652 0.5693208030491013 chr10 135534747 15388186 0.1135368334734118 1.9606481267502542 chr11 135006516 13472844 0.0997940277193732 0.626465764533176 chr12 133851895 15569666 0.11632010140760428 0.4212376180896982 chr13 115169878 8894461 0.07722905636836742 0.3195331832263591 chr14 107349540 6253687 0.058255368397479856 0.2970923263031317 chr15 102531392 7189723 0.07012216317125589 0.30672845019764877 chr16 90354753 8657977 0.09582204269873883 0.8497413178069398 chr17 81195210 7901098 0.09730990288712844 0.5362692459707162 chr18 78077248 6164699 0.07895640737747314 1.0303668769188823 chr19 59128983 4986556 0.08433353233895466 2.012529593103586 chr20 63025520 5186512 0.08229225240823082 0.34844312938265076 chr21 48129895 3807014 0.07909873894385185 0.3793554688803886 chr22 51304566 3204677 0.06246377759047801 0.2889611120933372 chrMT 16571 528784 31.91020457425623 18.081426769340997 chrX 155270560 12669513 0.08159636314830061 0.3896687539255105 chrY 59373566 769020 0.012952228606245413 0.5279762023127647