BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716389.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 = 639,446 number of mapped reads = 531,896 (83.18%) number of supplementary alignments = 3,424 (0.54%) number of secondary alignments = 0 number of mapped bases = 31,456,513 bp number of sequenced bases = 31,448,277 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 14,596 duplication rate = 2.28% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.36 >>>>>>> ACTG content number of A's = 7,954,596 bp (25.29%) number of C's = 6,173,359 bp (19.63%) number of T's = 9,750,289 bp (31%) number of G's = 7,569,840 bp (24.07%) number of N's = 193 bp (0%) GC percentage = 43.7% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 151,414 number of insertions = 2,488 mapped reads with insertion percentage = 0.47% number of deletions = 5,253 mapped reads with deletion percentage = 0.98% homopolymer indels = 43.25% >>>>>>> Coverage mean coverageData = 0.0102X std coverageData = 0.1233X There is a 0.94% of reference with a coverageData >= 1X There is a 0.06% of reference with a coverageData >= 2X There is a 0.01% 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 2533549 0.010164664745208399 0.15861776230895036 chr2 243199373 2601436 0.010696721656432888 0.1419001186932947 chr3 198022430 2074437 0.010475767820847366 0.10866220184567892 chr4 191154276 1998071 0.010452661807052645 0.1161742903182042 chr5 180915260 1883497 0.010410934931635949 0.10877117018456937 chr6 171115067 1770644 0.010347680254246693 0.11291532249007877 chr7 159138663 1780508 0.011188406176316813 0.15183608324236525 chr8 146364022 1598220 0.010919486757476506 0.1413537498098396 chr9 141213431 1309262 0.00927151185782038 0.10988303347198865 chr10 135534747 1505578 0.01110842815827885 0.12564324112224753 chr11 135006516 1447267 0.010719978878649087 0.12077619531402842 chr12 133851895 1437601 0.010740236438191629 0.11058378092356684 chr13 115169878 957011 0.008309559900723348 0.09737066307258947 chr14 107349540 907288 0.008451717631952592 0.09932509828209163 chr15 102531392 921938 0.008991763225061842 0.1012312669003967 chr16 90354753 950547 0.01052016599503072 0.11135347996123295 chr17 81195210 889060 0.010949660700428018 0.1139859364309726 chr18 78077248 849962 0.010886167504264495 0.16055246440989412 chr19 59128983 667168 0.011283265264345914 0.13643826922134702 chr20 63025520 712734 0.011308657191563036 0.11507401335768697 chr21 48129895 412016 0.00856050070335703 0.10355121438738345 chr22 51304566 400948 0.007815054901741104 0.0941815965238015 chrMT 16571 17825 1.0756743708889023 1.263092249138828 chrX 155270560 1734520 0.011170952175351207 0.11527875825398895 chrY 59373566 95426 0.00160721355358713 0.05886015299994469