BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6230335.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 = 2,794,752 number of mapped reads = 2,162,415 (77.37%) number of supplementary alignments = 17,149 (0.61%) number of secondary alignments = 0 number of mapped bases = 141,340,927 bp number of sequenced bases = 141,280,452 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 155,758 duplication rate = 5.91% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.2946 >>>>>>> ACTG content number of A's = 38,863,256 bp (27.51%) number of C's = 24,104,455 bp (17.06%) number of T's = 48,076,593 bp (34.03%) number of G's = 29,971,886 bp (21.21%) number of N's = 264,262 bp (0.19%) GC percentage = 38.28% >>>>>>> Mismatches and indels general error rate = 0.0114 number of mismatches = 1,588,360 number of insertions = 12,638 mapped reads with insertion percentage = 0.58% number of deletions = 37,047 mapped reads with deletion percentage = 1.69% homopolymer indels = 48.67% >>>>>>> Coverage mean coverageData = 0.0457X std coverageData = 0.409X There is a 3.41% of reference with a coverageData >= 1X There is a 0.78% of reference with a coverageData >= 2X There is a 0.2% of reference with a coverageData >= 3X There is a 0.06% 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 0.01% of reference with a coverageData >= 7X There is a 0.01% 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 14019234 0.056245532884750565 0.6636491450448395 chr2 243199373 10986178 0.0451735457393634 0.39177412365794745 chr3 198022430 10106729 0.0510383040951472 0.28640970530829196 chr4 191154276 8344288 0.04365211270502785 0.2945211694229129 chr5 180915260 8782133 0.04854279843502422 0.27946241876179695 chr6 171115067 7327499 0.04282205610801064 0.3837026353744494 chr7 159138663 3423822 0.021514708842313195 0.23251338382828704 chr8 146364022 6535874 0.044654922095540665 0.747839868030463 chr9 141213431 11416804 0.08084786212722216 0.48299395414690505 chr10 135534747 9013202 0.06650104271785005 0.44294159631632574 chr11 135006516 1942713 0.014389772120332326 0.19190901773087174 chr12 133851895 4762018 0.03557676938380289 0.2512491705957833 chr13 115169878 6813041 0.059156448876328586 0.3118669530632366 chr14 107349540 4414873 0.04112614735004919 0.2895806344052402 chr15 102531392 1508737 0.014714878736845785 0.15088370369673265 chr16 90354753 2650856 0.029338312728274515 0.24202715735764507 chr17 81195210 1832775 0.022572452241948756 0.21039354484432693 chr18 78077248 3057194 0.039156016359593 0.633327370998923 chr19 59128983 1106916 0.018720362567372417 0.4497579958561491 chr20 63025520 1209218 0.019186164588566663 0.19046247767563385 chr21 48129895 944990 0.01963415876972098 0.23191315008176652 chr22 51304566 474616 0.009250950490449524 0.11535736364994378 chrMT 16571 156310 9.432743950274576 5.774068480409374 chrX 155270560 20059562 0.12919101985592119 0.5635163991834755 chrY 59373566 451345 0.007601783595076637 0.16588923998376837