BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716653.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 = 1,044,023 number of mapped reads = 832,361 (79.73%) number of supplementary alignments = 23,754 (2.28%) number of secondary alignments = 0 number of mapped bases = 62,459,275 bp number of sequenced bases = 62,437,197 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 14,543 duplication rate = 1.14% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.7818 >>>>>>> ACTG content number of A's = 16,377,951 bp (26.23%) number of C's = 12,787,947 bp (20.48%) number of T's = 18,208,378 bp (29.16%) number of G's = 15,055,246 bp (24.11%) number of N's = 7,675 bp (0.01%) GC percentage = 44.59% >>>>>>> Mismatches and indels general error rate = 0.0079 number of mismatches = 481,164 number of insertions = 5,628 mapped reads with insertion percentage = 0.67% number of deletions = 12,650 mapped reads with deletion percentage = 1.5% homopolymer indels = 40.26% >>>>>>> Coverage mean coverageData = 0.0202X std coverageData = 0.1899X There is a 1.87% of reference with a coverageData >= 1X There is a 0.11% 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 6360145 0.02551706781906072 0.2406703207958619 chr2 243199373 5114200 0.021028837109707516 0.27809807059133845 chr3 198022430 5368456 0.027110343005082808 0.17721030088050962 chr4 191154276 2527493 0.013222267651496323 0.12816454406197472 chr5 180915260 3746551 0.020708872209011003 0.15309938446172078 chr6 171115067 3827926 0.02237047892457068 0.16853797393551415 chr7 159138663 2992734 0.018805825960722066 0.22551348046846034 chr8 146364022 3800043 0.02596295830132353 0.23053515230217128 chr9 141213431 3229581 0.02287021126198683 0.19218087096194425 chr10 135534747 3402941 0.02510751726271345 0.20378741353275306 chr11 135006516 2968093 0.02198481294043615 0.1746727498263977 chr12 133851895 2220442 0.016588797640855215 0.13576920354187613 chr13 115169878 1858427 0.016136398095342255 0.13353968553489223 chr14 107349540 1302073 0.012129283460366947 0.12143120639797618 chr15 102531392 1283816 0.012521199361069827 0.11725917192370103 chr16 90354753 1643647 0.01819104081884879 0.15134088172653057 chr17 81195210 1996631 0.02459050232150394 0.17382284934841669 chr18 78077248 1927709 0.02468976621716995 0.2770772198878325 chr19 59128983 1013198 0.017135386888017336 0.22188747326261435 chr20 63025520 1130228 0.017932862751469564 0.14648662631119894 chr21 48129895 1303545 0.0270838945316627 0.1779155909054049 chr22 51304566 1004733 0.01958369553306425 0.14949001767264963 chrMT 16571 83588 5.044233902600929 3.805550090567024 chrX 155270560 2213129 0.01425337166298621 0.13942770999994422 chrY 59373566 139946 0.0023570421894484155 0.0773507749869366