BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716912.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 = 1,247,912 number of mapped reads = 1,095,982 (87.83%) number of supplementary alignments = 3,948 (0.32%) number of secondary alignments = 0 number of mapped bases = 63,201,856 bp number of sequenced bases = 63,182,033 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 28,172 duplication rate = 1.89% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.9143 >>>>>>> ACTG content number of A's = 15,984,570 bp (25.3%) number of C's = 11,666,057 bp (18.46%) number of T's = 19,499,754 bp (30.86%) number of G's = 16,031,174 bp (25.37%) number of N's = 478 bp (0%) GC percentage = 43.84% >>>>>>> Mismatches and indels general error rate = 0.0054 number of mismatches = 330,282 number of insertions = 4,611 mapped reads with insertion percentage = 0.42% number of deletions = 12,355 mapped reads with deletion percentage = 1.12% homopolymer indels = 40.6% >>>>>>> Coverage mean coverageData = 0.0204X std coverageData = 0.1908X There is a 1.87% of reference with a coverageData >= 1X There is a 0.12% of reference with a coverageData >= 2X There is a 0.02% 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 5163728 0.020717011573664245 0.23491977374498743 chr2 243199373 5437876 0.022359745146217955 0.27752819338815904 chr3 198022430 4304831 0.021739108039427656 0.15936008697658627 chr4 191154276 4073637 0.021310729141104854 0.1703877229300199 chr5 180915260 3780922 0.020898856182723337 0.15426425148200495 chr6 171115067 3722587 0.02175487562413192 0.17474644198848216 chr7 159138663 3594157 0.02258506469920512 0.23362843081048332 chr8 146364022 3240479 0.022139860299821495 0.18861408190503628 chr9 141213431 2721653 0.019273329602762786 0.16901779422679988 chr10 135534747 3180813 0.02346861650171524 0.23200579329535725 chr11 135006516 2900601 0.021484896329003852 0.18339736972636916 chr12 133851895 2964516 0.02214773276089965 0.15967053456352368 chr13 115169878 1995576 0.017327238985179787 0.14091636823385584 chr14 107349540 1959783 0.018256091269697104 0.15024498899933866 chr15 102531392 1891123 0.018444331663808874 0.14846900000501703 chr16 90354753 1973766 0.021844628361719944 0.16866299343276325 chr17 81195210 1846766 0.02274476536239022 0.16495087747725004 chr18 78077248 1677909 0.021490370664703756 0.252794466877402 chr19 59128983 1453391 0.024580010111115897 0.22070003890987128 chr20 63025520 1429597 0.022682827527642772 0.16545445718555327 chr21 48129895 841945 0.01749318173247625 0.15332533672628998 chr22 51304566 807279 0.01573503223865104 0.13501118124997966 chrMT 16571 21442 1.2939472572566533 1.4129353320100488 chrX 155270560 2034185 0.013100905928335673 0.13404216475951225 chrY 59373566 183294 0.0030871314012030204 0.10612596353730609