BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716336.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 = 456,662 number of mapped reads = 411,903 (90.2%) number of supplementary alignments = 1,507 (0.33%) number of secondary alignments = 0 number of mapped bases = 23,994,254 bp number of sequenced bases = 23,987,604 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 8,207 duplication rate = 1.63% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.1054 >>>>>>> ACTG content number of A's = 6,513,051 bp (27.15%) number of C's = 4,470,834 bp (18.64%) number of T's = 7,294,631 bp (30.41%) number of G's = 5,708,724 bp (23.8%) number of N's = 364 bp (0%) GC percentage = 42.44% >>>>>>> Mismatches and indels general error rate = 0.0054 number of mismatches = 125,785 number of insertions = 1,890 mapped reads with insertion percentage = 0.46% number of deletions = 3,957 mapped reads with deletion percentage = 0.95% homopolymer indels = 43.25% >>>>>>> Coverage mean coverageData = 0.0078X std coverageData = 0.1046X There is a 0.74% of reference with a coverageData >= 1X There is a 0.02% of reference with a coverageData >= 2X There is a 0% 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 1984857 0.007963298113508011 0.1522151594733177 chr2 243199373 2099360 0.008632259097148248 0.11060878341842684 chr3 198022430 1681428 0.008491098710383465 0.0948706310851774 chr4 191154276 1722388 0.009010460221146191 0.09919932766577674 chr5 180915260 1490919 0.008240979782468322 0.09386108681063167 chr6 171115067 1414258 0.008264953079789287 0.0958082109207494 chr7 159138663 1315472 0.008266199898889435 0.11354109873770034 chr8 146364022 1238985 0.008465092603153526 0.11927086804003356 chr9 141213431 1015483 0.007191121926638833 0.09929033436994328 chr10 135534747 1163217 0.008582426468099726 0.10604841110666416 chr11 135006516 1076523 0.007973859572822397 0.1021398190941204 chr12 133851895 1125034 0.008405065912589433 0.09515409136869467 chr13 115169878 762803 0.00662328564765867 0.08358534364669468 chr14 107349540 731577 0.006814905774165404 0.08740949934577608 chr15 102531392 687904 0.0067092037529345155 0.08391368519679157 chr16 90354753 690374 0.007640704855891754 0.09158247135070081 chr17 81195210 644498 0.007937635729989491 0.09310841685030671 chr18 78077248 694659 0.008897073318977636 0.14191749100132 chr19 59128983 464285 0.00785207146214573 0.12831480675469573 chr20 63025520 552565 0.008767321554824141 0.0972007544840922 chr21 48129895 309402 0.0064284785994234974 0.08470099069987538 chr22 51304566 258110 0.005030936232849139 0.07255533943408135 chrMT 16571 8292 0.5003922515237463 0.7640127716800421 chrX 155270560 800722 0.00515694668712472 0.07768917179325216 chrY 59373566 61139 0.0010297343433945 0.04039270347331534