BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716346.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 = 1,086,091 number of mapped reads = 1,028,685 (94.71%) number of supplementary alignments = 20,128 (1.85%) number of secondary alignments = 0 number of mapped bases = 81,720,404 bp number of sequenced bases = 81,681,491 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 30,652 duplication rate = 2.05% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.5106 >>>>>>> ACTG content number of A's = 20,609,551 bp (25.23%) number of C's = 16,321,181 bp (19.98%) number of T's = 24,712,161 bp (30.25%) number of G's = 20,032,867 bp (24.53%) number of N's = 5,731 bp (0.01%) GC percentage = 44.51% >>>>>>> Mismatches and indels general error rate = 0.0065 number of mismatches = 514,736 number of insertions = 6,316 mapped reads with insertion percentage = 0.6% number of deletions = 20,330 mapped reads with deletion percentage = 1.95% homopolymer indels = 43.27% >>>>>>> Coverage mean coverageData = 0.0264X std coverageData = 0.2769X There is a 2.37% of reference with a coverageData >= 1X There is a 0.18% of reference with a coverageData >= 2X There is a 0.03% of reference with a coverageData >= 3X There is a 0.01% 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 7940077 0.03185579625897903 0.5614955831689058 chr2 243199373 6761289 0.027801424471600097 0.2901405159813857 chr3 198022430 5196253 0.026240729396159818 0.17318491741007083 chr4 191154276 5094847 0.02665306320429892 0.20640159839433325 chr5 180915260 4674613 0.025838688234480607 0.17279565372586023 chr6 171115067 4457868 0.026051873035820978 0.18218254059397712 chr7 159138663 4304742 0.027050258679124382 0.3195398483165196 chr8 146364022 4057700 0.027723343104086057 0.2969960292680493 chr9 141213431 3299865 0.02336792595882753 0.2294500760975105 chr10 135534747 3749567 0.027664986898156826 0.2787424020132349 chr11 135006516 4492353 0.03327508281155852 0.3029120212847023 chr12 133851895 3542632 0.02646680497127067 0.17516045957403184 chr13 115169878 2864877 0.024875228225908166 0.1691073344406684 chr14 107349540 2363587 0.022017672362638907 0.16992620865235475 chr15 102531392 2238196 0.021829372998271594 0.15756226960058775 chr16 90354753 1823283 0.020179159805793503 0.1625127609663888 chr17 81195210 2948401 0.03631249922255266 0.2397046258827598 chr18 78077248 2082043 0.026666449616666817 0.38108542258307404 chr19 59128983 1530885 0.025890602583169747 0.40874442170829967 chr20 63025520 1650573 0.02618896282014016 0.17829094250663166 chr21 48129895 1068965 0.022210000665906292 0.18160927314621947 chr22 51304566 912213 0.017780347269675763 0.14288122202969022 chrMT 16571 3788 0.2285921187616921 0.5901906205349418 chrX 155270560 4421489 0.028476029197035162 0.20294221476574514 chrY 59373566 240298 0.004047221957326936 0.1445391357009514