BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238072.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 2,090,489 number of mapped reads = 1,855,491 (88.76%) number of supplementary alignments = 20,058 (0.96%) number of secondary alignments = 0 number of mapped bases = 123,951,652 bp number of sequenced bases = 123,898,528 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 106,294 duplication rate = 4.34% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.3881 >>>>>>> ACTG content number of A's = 33,592,122 bp (27.11%) number of C's = 23,861,258 bp (19.26%) number of T's = 38,327,046 bp (30.93%) number of G's = 28,110,959 bp (22.69%) number of N's = 7,143 bp (0.01%) GC percentage = 41.95% >>>>>>> Mismatches and indels general error rate = 0.0076 number of mismatches = 922,698 number of insertions = 9,532 mapped reads with insertion percentage = 0.51% number of deletions = 29,131 mapped reads with deletion percentage = 1.55% homopolymer indels = 45.9% >>>>>>> Coverage mean coverageData = 0.04X std coverageData = 0.4542X There is a 3.04% of reference with a coverageData >= 1X There is a 0.66% of reference with a coverageData >= 2X There is a 0.16% of reference with a coverageData >= 3X There is a 0.05% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% 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 13373802 0.05365604284693036 1.0602455815190277 chr2 243199373 15067709 0.06195620002688083 0.4547085255061645 chr3 198022430 10533982 0.05319590311057187 0.2876610889016699 chr4 191154276 4339125 0.022699596842918647 0.24400477474996493 chr5 180915260 4904226 0.02710786254293861 0.21422921316888838 chr6 171115067 5976722 0.03492808730864127 0.24786668651287022 chr7 159138663 4168705 0.026195425557898524 0.22711840836152394 chr8 146364022 2615194 0.017867738015562323 0.5021729113022819 chr9 141213431 9618995 0.06811671476206821 0.44912514393395 chr10 135534747 3535824 0.026087952191329946 0.3595366761507973 chr11 135006516 2245181 0.01663016768760998 0.21067659812120634 chr12 133851895 4126722 0.03083050860056931 0.2354701559910957 chr13 115169878 8360420 0.07259207134004257 0.3378097828151072 chr14 107349540 3609543 0.03362420556250171 0.279599548098387 chr15 102531392 8697763 0.08483024399005526 0.36926723351565016 chr16 90354753 5108601 0.05653937209036474 0.36179481029515115 chr17 81195210 6254991 0.0770364532587575 0.352633158295012 chr18 78077248 1524241 0.019522217278969668 0.8623237531783534 chr19 59128983 1294389 0.021890939676740256 0.5581773627974778 chr20 63025520 683231 0.010840545226758938 0.1728006620228422 chr21 48129895 2705858 0.056219902412004016 0.35326463195886826 chr22 51304566 2651152 0.051674776860991284 0.2876283021995071 chrMT 16571 64833 3.912437390622171 3.074105276538759 chrX 155270560 2104757 0.013555415785194567 0.174180391783281 chrY 59373566 385686 0.006495921097277532 0.27175377293275005