BamQC report ----------------------------------- >>>>>>> Input bam file = ERR9714100.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/ERP137498/ERP137498.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 = 549,398 number of mapped reads = 441,074 (80.28%) number of supplementary alignments = 13,709 (2.5%) number of secondary alignments = 0 number of mapped bases = 57,629,727 bp number of sequenced bases = 56,240,590 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 377,672 duplication rate = 43.94% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 51.5031 >>>>>>> ACTG content number of A's = 15,760,166 bp (28.02%) number of C's = 11,647,550 bp (20.71%) number of T's = 15,060,506 bp (26.78%) number of G's = 13,771,874 bp (24.49%) number of N's = 494 bp (0%) GC percentage = 45.2% >>>>>>> Mismatches and indels general error rate = 0.0476 number of mismatches = 2,491,600 number of insertions = 66,189 mapped reads with insertion percentage = 14.34% number of deletions = 222,997 mapped reads with deletion percentage = 46.54% homopolymer indels = 29.57% >>>>>>> Coverage mean coverageData = 0.0186X std coverageData = 3.8697X There is a 0.06% of reference with a coverageData >= 1X There is a 0.04% of reference with a coverageData >= 2X There is a 0.03% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.02% of reference with a coverageData >= 8X There is a 0.02% of reference with a coverageData >= 9X There is a 0.02% of reference with a coverageData >= 10X There is a 0.02% of reference with a coverageData >= 11X There is a 0.02% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 3341552 0.013406393880158076 2.0545262735519874 chr2 243199373 6242997 0.0256702841088328 8.00606678627195 chr3 198022430 3747906 0.018926674114644486 3.785409484472669 chr4 191154276 1896610 0.009921881109266947 1.5875809427041008 chr5 180915260 3362173 0.018584242147400943 3.1499734660650867 chr6 171115067 2634856 0.015398153103607176 2.2994351531806725 chr7 159138663 2270859 0.014269687561720939 2.1790538445801433 chr8 146364022 3713119 0.025369069182862438 5.53979436223276 chr9 141213431 2049011 0.014510029148714614 2.5191511021089616 chr10 135534747 2722848 0.02008966748578503 3.2026195359391116 chr11 135006516 2980133 0.022073993821157493 4.6247097943479964 chr12 133851895 2430698 0.018159608423922575 2.6622702059078676 chr13 115169878 2049207 0.017792907621209775 3.6529873685587764 chr14 107349540 1826558 0.017015051950851397 2.6956263332210004 chr15 102531392 1441737 0.014061420330663217 1.7339711681608403 chr16 90354753 1409685 0.015601669565739391 1.8999009177916915 chr17 81195210 1548164 0.019067183889295933 3.3355180049451802 chr18 78077248 1279675 0.016389857900729287 2.534944066687972 chr19 59128983 997296 0.016866449402655886 3.496598552648366 chr20 63025520 1110396 0.017618196565454755 2.74232728176285 chr21 48129895 658777 0.013687480514968918 3.364126569015938 chr22 51304566 494574 0.009639960700573902 1.194102197265107 chrMT 16571 294318 17.761028302456097 135.92732385324646 chrX 155270560 7023930 0.045236714545242834 6.132636586968204 chrY 59373566 102648 0.0017288501755141337 0.27788875388211404