BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6008822.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 = 2,292,738 number of mapped reads = 1,765,981 (77.02%) number of supplementary alignments = 11,505 (0.5%) number of secondary alignments = 0 number of mapped bases = 114,479,954 bp number of sequenced bases = 114,422,157 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 107,872 duplication rate = 5% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 34.4461 >>>>>>> ACTG content number of A's = 31,492,767 bp (27.52%) number of C's = 21,550,246 bp (18.83%) number of T's = 35,736,772 bp (31.23%) number of G's = 25,479,419 bp (22.27%) number of N's = 162,953 bp (0.14%) GC percentage = 41.1% >>>>>>> Mismatches and indels general error rate = 0.0081 number of mismatches = 915,562 number of insertions = 7,585 mapped reads with insertion percentage = 0.43% number of deletions = 32,295 mapped reads with deletion percentage = 1.81% homopolymer indels = 46.06% >>>>>>> Coverage mean coverageData = 0.037X std coverageData = 0.3513X There is a 2.74% of reference with a coverageData >= 1X There is a 0.66% of reference with a coverageData >= 2X There is a 0.18% 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% 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 14062709 0.056419955719989964 0.3997738922938548 chr2 243199373 6606773 0.027166077438859185 0.2924140976678899 chr3 198022430 14789996 0.07468848857172392 0.3824324721437899 chr4 191154276 19280319 0.10086260900593194 0.41546164021567805 chr5 180915260 815328 0.004506684510748292 0.08192660722040952 chr6 171115067 684689 0.004001336714551267 0.09388671905773507 chr7 159138663 13195791 0.08292008209218146 0.4278461929451302 chr8 146364022 10625672 0.07259756772740229 0.6684359004571787 chr9 141213431 1146551 0.00811927726619715 0.16494630530163024 chr10 135534747 2481274 0.018307290602018092 0.8176354237010223 chr11 135006516 1046525 0.007751662890108208 0.15419878977956478 chr12 133851895 471005 0.003518851937060734 0.08395965818196338 chr13 115169878 470064 0.004081483875497376 0.07957252771754612 chr14 107349540 7689214 0.07162782439496247 0.3501172591540355 chr15 102531392 4764117 0.046464959726675706 0.28732277271971307 chr16 90354753 417314 0.004618617019516395 0.1729646282316057 chr17 81195210 2501097 0.030803504295388855 0.22145462279404246 chr18 78077248 1248748 0.01599375018955586 0.32767531681665063 chr19 59128983 4421941 0.07478466186370904 0.38027413749851446 chr20 63025520 1629330 0.025851908877546747 0.212414551788407 chr21 48129895 1542781 0.032054526609709 0.24277881962426429 chr22 51304566 2372483 0.046243116061053906 0.27179851457849635 chrMT 16571 75792 4.573773459658439 4.084164407011706 chrX 155270560 1963527 0.012645842199577305 0.15172336717821508 chrY 59373566 176914 0.0029796761744106796 0.12434776953075674