BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716559.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 = 19,461,283 number of mapped reads = 18,790,385 (96.55%) number of supplementary alignments = 10,195 (0.05%) number of secondary alignments = 0 number of mapped bases = 1,277,646,077 bp number of sequenced bases = 1,277,426,916 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 932,197 duplication rate = 1.71% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.1498 >>>>>>> ACTG content number of A's = 365,999,099 bp (28.65%) number of C's = 262,684,814 bp (20.56%) number of T's = 384,737,702 bp (30.12%) number of G's = 263,941,379 bp (20.66%) number of N's = 63,922 bp (0.01%) GC percentage = 41.23% >>>>>>> Mismatches and indels general error rate = 0.0032 number of mismatches = 3,859,383 number of insertions = 112,872 mapped reads with insertion percentage = 0.6% number of deletions = 111,218 mapped reads with deletion percentage = 0.59% homopolymer indels = 38.59% >>>>>>> Coverage mean coverageData = 0.4127X std coverageData = 4.5528X There is a 31.18% of reference with a coverageData >= 1X There is a 6.68% of reference with a coverageData >= 2X There is a 1.21% of reference with a coverageData >= 3X There is a 0.27% of reference with a coverageData >= 4X There is a 0.11% of reference with a coverageData >= 5X There is a 0.06% of reference with a coverageData >= 6X There is a 0.04% of reference with a coverageData >= 7X There is a 0.03% of reference with a coverageData >= 8X There is a 0.03% of reference with a coverageData >= 9X There is a 0.02% of reference with a coverageData >= 10X There is a 0.02% of reference with a coverageData >= 11X There is a 0.02% of reference with a coverageData >= 12X There is a 0.02% of reference with a coverageData >= 13X There is a 0.02% of reference with a coverageData >= 14X There is a 0.02% of reference with a coverageData >= 15X There is a 0.02% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 98399912 0.3947830164082119 11.4176108104025 chr2 243199373 105475015 0.4336977258572126 3.159079740575881 chr3 198022430 78870248 0.39828946650134534 1.6889014427901456 chr4 191154276 81803342 0.427944086377644 2.431000223559352 chr5 180915260 72025741 0.3981186606370297 0.7788648525936738 chr6 171115067 68086025 0.39789614201536094 1.4893350101706917 chr7 159138663 75302714 0.4731893091247097 3.345547935889477 chr8 146364022 58336611 0.39857206848278603 2.5369943835430515 chr9 141213431 55858623 0.3955616870466096 2.483145254307976 chr10 135534747 61612469 0.4545879958000733 10.034310860530313 chr11 135006516 52511440 0.38895485607524305 1.6538189781433508 chr12 133851895 76202099 0.5693016075715626 1.174583333734285 chr13 115169878 43894043 0.38112433356923414 0.6553095751505587 chr14 107349540 41940495 0.39069096150761334 1.154057198073766 chr15 102531392 33386996 0.325627062587817 0.6137866043477263 chr16 90354753 41634118 0.46078503473967775 3.899486052522928 chr17 81195210 37728763 0.4646673492192458 1.2358773968537604 chr18 78077248 37069837 0.4747841138048308 5.232809456556504 chr19 59128983 24760726 0.4187578534878572 8.027436182042617 chr20 63025520 33498918 0.5315135519706937 1.1841625641596996 chr21 48129895 16621591 0.3453485822065475 2.31529325572529 chr22 51304566 14353488 0.2797701865366135 0.6759717151957801 chrMT 16571 1834806 110.72391527367087 26.744068981069933 chrX 155270560 61504455 0.39611150368749876 1.3468432798403496 chrY 59373566 4933602 0.08309425106789105 3.4647460041897293