BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716178.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 = 973,626 number of mapped reads = 885,942 (90.99%) number of supplementary alignments = 17,417 (1.79%) number of secondary alignments = 0 number of mapped bases = 69,883,931 bp number of sequenced bases = 69,852,064 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 23,248 duplication rate = 1.89% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.6378 >>>>>>> ACTG content number of A's = 18,642,819 bp (26.69%) number of C's = 13,163,369 bp (18.84%) number of T's = 21,192,848 bp (30.34%) number of G's = 16,848,325 bp (24.12%) number of N's = 4,703 bp (0.01%) GC percentage = 42.96% >>>>>>> Mismatches and indels general error rate = 0.0067 number of mismatches = 454,532 number of insertions = 6,065 mapped reads with insertion percentage = 0.67% number of deletions = 16,760 mapped reads with deletion percentage = 1.86% homopolymer indels = 42.17% >>>>>>> Coverage mean coverageData = 0.0226X std coverageData = 0.2179X There is a 2.06% of reference with a coverageData >= 1X There is a 0.14% of reference with a coverageData >= 2X There is a 0.02% 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 5674823 0.022767538059614303 0.3509916434007808 chr2 243199373 5852756 0.024065670596938586 0.2570597484792189 chr3 198022430 4549162 0.0229729632143187 0.16100031257679412 chr4 191154276 4545732 0.02378043586113658 0.19482651792022002 chr5 180915260 4182799 0.023120211086671186 0.16255290776912357 chr6 171115067 4004341 0.023401451842928595 0.17157460629681665 chr7 159138663 3851712 0.02420349604168787 0.27142531226354544 chr8 146364022 3594347 0.02455758560665954 0.2618077219503027 chr9 141213431 2926010 0.02072047948470284 0.1983103426413457 chr10 135534747 3392758 0.02503238523771325 0.2337125116780655 chr11 135006516 3197204 0.023681849548654377 0.21660355973995601 chr12 133851895 3130611 0.023388619189888944 0.1635863156563039 chr13 115169878 2208284 0.019174145517459 0.14695293867746517 chr14 107349540 2088050 0.019450945015693593 0.1539718044442772 chr15 102531392 2038956 0.01988616325427436 0.14998254655465976 chr16 90354753 2046919 0.022654248194336826 0.1682900680114882 chr17 81195210 1902595 0.023432355184499185 0.17521387939282487 chr18 78077248 1882764 0.024114118366467013 0.2929849343549479 chr19 59128983 1420668 0.024026592847030702 0.26123205795436144 chr20 63025520 1498074 0.023769323918311186 0.17029262312805263 chr21 48129895 927371 0.01926808691354926 0.16408435979960084 chr22 51304566 827430 0.016127804297184776 0.13543325204647474 chrMT 16571 5870 0.35423329913704665 0.6158376094893634 chrX 155270560 3928649 0.025301956790778627 0.1831531967390626 chrY 59373566 206046 0.00347033223505558 0.12898578165478947