BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716532.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 = 1,688,861 number of mapped reads = 1,595,852 (94.49%) number of supplementary alignments = 33,403 (1.98%) number of secondary alignments = 0 number of mapped bases = 123,764,251 bp number of sequenced bases = 123,710,911 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 59,272 duplication rate = 2.62% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.9758 >>>>>>> ACTG content number of A's = 31,808,541 bp (25.71%) number of C's = 24,651,035 bp (19.93%) number of T's = 37,514,809 bp (30.32%) number of G's = 29,728,326 bp (24.03%) number of N's = 8,200 bp (0.01%) GC percentage = 43.96% >>>>>>> Mismatches and indels general error rate = 0.0063 number of mismatches = 761,446 number of insertions = 8,823 mapped reads with insertion percentage = 0.55% number of deletions = 28,148 mapped reads with deletion percentage = 1.74% homopolymer indels = 43.29% >>>>>>> Coverage mean coverageData = 0.04X std coverageData = 0.3954X There is a 3.46% of reference with a coverageData >= 1X There is a 0.37% of reference with a coverageData >= 2X There is a 0.06% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% 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 12450413 0.04995138206696785 0.8569051588618669 chr2 243199373 10547508 0.04336979931276385 0.4212592748357721 chr3 198022430 8089891 0.04085340736400417 0.22429155382571586 chr4 191154276 7996836 0.041834460454340035 0.26454415474904724 chr5 180915260 7429208 0.04106457354675332 0.22675140661301466 chr6 171115067 7056078 0.041235866155491734 0.24512946931769414 chr7 159138663 6677445 0.04195991642835406 0.4639126562318839 chr8 146364022 3445810 0.023542739212236187 0.3992987079028656 chr9 141213431 5117165 0.036237098438603906 0.30963307962377873 chr10 135534747 5831457 0.043025549750721856 0.3820501978106486 chr11 135006516 6971392 0.05163744837323259 0.4254091052864974 chr12 133851895 5456551 0.04076558647152512 0.2256459316602611 chr13 115169878 4406931 0.03826461464168608 0.2194606197507164 chr14 107349540 3672926 0.03421464125509993 0.22286557404183474 chr15 102531392 3537830 0.03450484706186375 0.20707904067405092 chr16 90354753 2800197 0.03099114221473219 0.2137877329519985 chr17 81195210 3825244 0.04711169538203054 0.31032410423445866 chr18 78077248 3280594 0.042017285240381425 0.5273422113284137 chr19 59128983 2356477 0.039853163041887595 0.6114937007805675 chr20 63025520 2488010 0.0394762312155457 0.22742704122845822 chr21 48129895 1607692 0.03340318943143342 0.23047809194712002 chr22 51304566 1354466 0.02640049620534749 0.17951644243912077 chrMT 16571 23859 1.4398044777020096 1.411361610582189 chrX 155270560 6990969 0.04502443347921203 0.2797753971321248 chrY 59373566 349302 0.0058831231393445356 0.17904021371543966