BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716098.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 = 866,646 number of mapped reads = 774,634 (89.38%) number of supplementary alignments = 2,979 (0.34%) number of secondary alignments = 0 number of mapped bases = 44,718,761 bp number of sequenced bases = 44,705,333 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 21,700 duplication rate = 2.17% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.1177 >>>>>>> ACTG content number of A's = 11,485,660 bp (25.69%) number of C's = 8,309,733 bp (18.59%) number of T's = 14,405,147 bp (32.22%) number of G's = 10,503,485 bp (23.49%) number of N's = 1,308 bp (0%) GC percentage = 42.08% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 225,967 number of insertions = 3,404 mapped reads with insertion percentage = 0.44% number of deletions = 8,428 mapped reads with deletion percentage = 1.08% homopolymer indels = 42.76% >>>>>>> Coverage mean coverageData = 0.0144X std coverageData = 0.1614X There is a 1.34% of reference with a coverageData >= 1X There is a 0.07% 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 3607920 0.014475069251683029 0.26759484655895055 chr2 243199373 3770505 0.015503761187739575 0.20829774970037 chr3 198022430 2966711 0.014981691720478332 0.12954234783407 chr4 191154276 2887227 0.015104171669170509 0.1344400765899484 chr5 180915260 2690975 0.014874228962222425 0.12882675247026748 chr6 171115067 2538078 0.014832580464699815 0.14117896948556818 chr7 159138663 2498628 0.01570094880085803 0.1806180210840499 chr8 146364022 2259944 0.015440570497577608 0.15803143775973158 chr9 141213431 1858785 0.0131629476519128 0.1365172225417379 chr10 135534747 2148686 0.01585339588231201 0.15876329588655716 chr11 135006516 2003912 0.014843076166782942 0.141376037890227 chr12 133851895 2035331 0.015205843742443841 0.13181728622784297 chr13 115169878 1408781 0.012232200159142306 0.11695315466770372 chr14 107349540 1380724 0.012861946124780785 0.12405870365177535 chr15 102531392 1277475 0.012459354887135444 0.12019048808078425 chr16 90354753 1316069 0.014565575758919954 0.1320976671549771 chr17 81195210 1207785 0.014875076990379113 0.13144485208382856 chr18 78077248 1174872 0.015047559053310896 0.20457768165091791 chr19 59128983 948779 0.01604592116864246 0.19693128524584608 chr20 63025520 937256 0.014871055407396876 0.12953474178950716 chr21 48129895 580200 0.012054877742824911 0.12051306025793497 chr22 51304566 532246 0.010374242323772898 0.10717111395409334 chrMT 16571 18723 1.1298654275541609 1.2125271205546713 chrX 155270560 2524758 0.01626037801370717 0.14300990559970464 chrY 59373566 144391 0.002431907155450289 0.0764019906859903