BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238240.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 = 1,053,651 number of mapped reads = 560,084 (53.16%) number of supplementary alignments = 6,129 (0.58%) number of secondary alignments = 0 number of mapped bases = 34,978,546 bp number of sequenced bases = 34,964,423 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 68,979 duplication rate = 8.53% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.9637 >>>>>>> ACTG content number of A's = 9,776,277 bp (27.96%) number of C's = 6,959,228 bp (19.9%) number of T's = 10,492,151 bp (30.01%) number of G's = 7,731,125 bp (22.11%) number of N's = 5,642 bp (0.02%) GC percentage = 42.02% >>>>>>> Mismatches and indels general error rate = 0.0092 number of mismatches = 317,144 number of insertions = 2,944 mapped reads with insertion percentage = 0.52% number of deletions = 8,579 mapped reads with deletion percentage = 1.52% homopolymer indels = 45.39% >>>>>>> Coverage mean coverageData = 0.0113X std coverageData = 0.2589X There is a 0.68% of reference with a coverageData >= 1X There is a 0.23% of reference with a coverageData >= 2X There is a 0.1% 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 2556236 0.010255685581621881 0.2791185800055505 chr2 243199373 2811348 0.011559848881682766 0.3594289624556208 chr3 198022430 2356482 0.011900076168139135 0.18855958065147224 chr4 191154276 2624674 0.01373065805757858 0.2190199218840021 chr5 180915260 1952375 0.010791654612220107 0.1860224242139931 chr6 171115067 2066118 0.012074436437558126 0.2590559357986043 chr7 159138663 1940864 0.012196055712746562 0.21073950913604883 chr8 146364022 1957253 0.0133725007912122 0.22424894678117324 chr9 141213431 1330970 0.00942523661223131 0.16749638797824706 chr10 135534747 1451348 0.010708309360698479 0.18837039348542192 chr11 135006516 1480281 0.010964515223842973 0.1758540431325099 chr12 133851895 1796218 0.013419443930920814 0.20227577544701086 chr13 115169878 996557 0.0086529309339027 0.21999347733993568 chr14 107349540 1076547 0.010028426763635875 0.46148779406596235 chr15 102531392 841739 0.00820957351286131 0.5522441295719741 chr16 90354753 972111 0.010758825271759639 0.18047209805565095 chr17 81195210 828148 0.010199468663237647 0.1767754467398915 chr18 78077248 871451 0.011161394930313118 0.1937160218359587 chr19 59128983 579717 0.009804278216657303 0.181228203320956 chr20 63025520 597669 0.009482968169084524 0.1626586223200667 chr21 48129895 918757 0.01908911290996999 0.23122424633860547 chr22 51304566 1032988 0.020134426241906034 0.318787272059317 chrMT 16571 19025 1.148090036811297 1.6155635981127425 chrX 155270560 1821696 0.011732397951034633 0.2534154165377065 chrY 59373566 97974 0.0016501282742559205 0.07087920148853637