BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238046.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 = 4,152,594 number of mapped reads = 176,272 (4.24%) number of supplementary alignments = 802 (0.02%) number of secondary alignments = 0 number of mapped bases = 10,319,251 bp number of sequenced bases = 10,313,215 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 11,205 duplication rate = 5.45% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.4314 >>>>>>> ACTG content number of A's = 2,593,891 bp (25.15%) number of C's = 1,729,626 bp (16.77%) number of T's = 3,355,760 bp (32.54%) number of G's = 2,633,479 bp (25.53%) number of N's = 459 bp (0%) GC percentage = 42.31% >>>>>>> Mismatches and indels general error rate = 0.0097 number of mismatches = 98,539 number of insertions = 758 mapped reads with insertion percentage = 0.43% number of deletions = 3,910 mapped reads with deletion percentage = 2.19% homopolymer indels = 48.35% >>>>>>> Coverage mean coverageData = 0.0033X std coverageData = 0.0693X There is a 0.29% of reference with a coverageData >= 1X There is a 0.03% of reference with a coverageData >= 2X There is a 0.01% 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 921028 0.0036951883863109813 0.07850558560438235 chr2 243199373 794508 0.003266899869844648 0.07931371246994882 chr3 198022430 902336 0.0045567363252738595 0.07857736808660076 chr4 191154276 609658 0.003189350574611263 0.06473774204018182 chr5 180915260 539057 0.0029796104540877315 0.06234059295426778 chr6 171115067 547866 0.0032017402652216474 0.06635470881806915 chr7 159138663 577944 0.003631700738870729 0.07656413180680145 chr8 146364022 508560 0.0034746243854927683 0.0687688437489141 chr9 141213431 429710 0.0030429825049714996 0.06509433339287203 chr10 135534747 447853 0.0033043408418359315 0.06761269164088986 chr11 135006516 392569 0.002907778169758858 0.0622596446799169 chr12 133851895 640859 0.004787821644213554 0.08080663936401926 chr13 115169878 425230 0.0036921980589403767 0.07023622015569357 chr14 107349540 301416 0.0028077996421782526 0.06081615380323863 chr15 102531392 316334 0.00308524046957248 0.06414076585917838 chr16 90354753 276293 0.003057869019906457 0.06365885199053595 chr17 81195210 242003 0.0029805083329423002 0.06219100462291078 chr18 78077248 253343 0.0032447736887447672 0.07382412114885621 chr19 59128983 185724 0.0031409977066576638 0.06663453419532302 chr20 63025520 208334 0.003305549878842729 0.0669639371571314 chr21 48129895 127991 0.0026592827597068307 0.05943313771548476 chr22 51304566 128656 0.0025076910308528873 0.057850135944445186 chrMT 16571 4823 0.2910506306197574 0.6527413498093819 chrX 155270560 506793 0.003263934901761158 0.06485242458618326 chrY 59373566 30363 5.113891929617298E-4 0.025427189927566964