BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524533.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 = 5,578,229 number of mapped reads = 5,130,303 (91.97%) number of supplementary alignments = 21,987 (0.39%) number of secondary alignments = 0 number of mapped bases = 295,499,097 bp number of sequenced bases = 295,421,446 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 364,688 duplication rate = 5.32% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.4203 >>>>>>> ACTG content number of A's = 75,921,020 bp (25.7%) number of C's = 57,895,639 bp (19.6%) number of T's = 91,936,460 bp (31.12%) number of G's = 69,659,601 bp (23.58%) number of N's = 8,726 bp (0%) GC percentage = 43.18% >>>>>>> Mismatches and indels general error rate = 0.0048 number of mismatches = 1,391,856 number of insertions = 18,232 mapped reads with insertion percentage = 0.35% number of deletions = 46,617 mapped reads with deletion percentage = 0.9% homopolymer indels = 43.73% >>>>>>> Coverage mean coverageData = 0.0955X std coverageData = 0.6938X There is a 7.29% of reference with a coverageData >= 1X There is a 1.48% of reference with a coverageData >= 2X There is a 0.38% of reference with a coverageData >= 3X There is a 0.12% of reference with a coverageData >= 4X There is a 0.05% of reference with a coverageData >= 5X There is a 0.03% of reference with a coverageData >= 6X There is a 0.02% 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 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% 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 22116148 0.0887305632831302 1.2642773564113878 chr2 243199373 22277680 0.09160253879437427 0.7810763171998892 chr3 198022430 18021984 0.09100981136328849 0.3716753707854774 chr4 191154276 17848627 0.09337288902708094 0.4831238675615452 chr5 180915260 15716753 0.08687356168849437 0.37449922194187396 chr6 171115067 16335496 0.0954649773768899 0.45497792320572794 chr7 159138663 18935329 0.11898635217263324 0.9892219050882416 chr8 146364022 13140463 0.08977932432056288 0.6185525464567081 chr9 141213431 13424353 0.09506427897782613 0.7219066795342882 chr10 135534747 11292377 0.08331721016161266 0.6941659014009637 chr11 135006516 11110916 0.08229910917781183 0.5738930883546757 chr12 133851895 21653369 0.1617711052951473 0.6381895429407092 chr13 115169878 11298175 0.09810008655214517 0.3887241507332951 chr14 107349540 10378925 0.09668346040420853 0.44831282924462634 chr15 102531392 7518878 0.0733324482710622 0.33587149512797354 chr16 90354753 8565256 0.09479585429224736 0.441084799140318 chr17 81195210 8923081 0.10989664291772877 0.4513870897165145 chr18 78077248 9319095 0.11935737028026398 1.3516382023600384 chr19 59128983 5280083 0.08929771377938295 0.9634665920529526 chr20 63025520 9224972 0.14636883598897715 0.5134078963395754 chr21 48129895 3558080 0.07392661047774984 0.4333717878616335 chr22 51304566 3022814 0.058919005376636455 0.2979743093363363 chrMT 16571 17987 1.0854504857884255 1.418740463066147 chrX 155270560 15704610 0.10114351361906597 0.5180771694351977 chrY 59373566 813646 0.013703842548382557 0.3041468045377725