BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524638.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 = 3,444,504 number of mapped reads = 3,107,407 (90.21%) number of supplementary alignments = 12,198 (0.35%) number of secondary alignments = 0 number of mapped bases = 180,924,891 bp number of sequenced bases = 180,864,603 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 305,463 duplication rate = 7.25% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.9525 >>>>>>> ACTG content number of A's = 43,184,071 bp (23.88%) number of C's = 32,233,492 bp (17.82%) number of T's = 59,826,308 bp (33.08%) number of G's = 45,619,319 bp (25.22%) number of N's = 1,413 bp (0%) GC percentage = 43.04% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 908,076 number of insertions = 13,159 mapped reads with insertion percentage = 0.42% number of deletions = 35,797 mapped reads with deletion percentage = 1.14% homopolymer indels = 43.04% >>>>>>> Coverage mean coverageData = 0.0584X std coverageData = 0.517X There is a 4.49% of reference with a coverageData >= 1X There is a 0.9% of reference with a coverageData >= 2X There is a 0.23% of reference with a coverageData >= 3X There is a 0.07% of reference with a coverageData >= 4X There is a 0.03% 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 0.01% of reference with a coverageData >= 8X There is a 0.01% 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 18419701 0.07390032139578902 1.021141164753538 chr2 243199373 16002840 0.06580132095982007 0.6333660271761864 chr3 198022430 12723109 0.06425084774487415 0.31838651614557567 chr4 191154276 7874077 0.04119226189844689 0.37943558704005 chr5 180915260 11090448 0.061301893494224866 0.31077832934554045 chr6 171115067 11599782 0.06778936655531333 0.35421152748529244 chr7 159138663 11043758 0.06939707668651206 0.6334328956592965 chr8 146364022 15416822 0.10533204669655771 0.6760266172949856 chr9 141213431 6423138 0.04548531931073893 0.39897601075036376 chr10 135534747 7483104 0.05521170154248342 0.581186840221365 chr11 135006516 9218616 0.06828274866377561 0.4180312849821844 chr12 133851895 6052511 0.04521797020505388 0.28090047798238954 chr13 115169878 3981840 0.03457362349554629 0.23739684758739366 chr14 107349540 3373808 0.03142824831853029 0.23555392784669824 chr15 102531392 4746439 0.046292544238548915 0.2744828995972968 chr16 90354753 5351179 0.05922410080629627 0.3374003944032407 chr17 81195210 4428637 0.05454308203648959 0.3119755636104822 chr18 78077248 4785086 0.06128656071484487 0.7097606534548044 chr19 59128983 3631287 0.06141297914763729 0.6814964032041192 chr20 63025520 3454466 0.05481059101138713 0.31199713379631727 chr21 48129895 1676933 0.034841817128418835 0.3382118531695445 chr22 51304566 3323101 0.06477203218130721 0.32529976630979923 chrMT 16571 96076 5.797839599299982 4.435922217699408 chrX 155270560 8144865 0.05245595172710139 0.33634990245668966 chrY 59373566 583268 0.00982369831045688 0.3823471211682447