BamQC report ----------------------------------- >>>>>>> Input bam file = ERR9714193.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 = 75,602 number of mapped reads = 21,367 (28.26%) number of supplementary alignments = 673 (0.89%) number of secondary alignments = 0 number of mapped bases = 2,299,546 bp number of sequenced bases = 2,260,905 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 17,867 duplication rate = 46.99% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 33.0175 >>>>>>> ACTG content number of A's = 466,843 bp (20.65%) number of C's = 390,854 bp (17.29%) number of T's = 431,322 bp (19.08%) number of G's = 971,841 bp (42.98%) number of N's = 45 bp (0%) GC percentage = 60.27% >>>>>>> Mismatches and indels general error rate = 0.036 number of mismatches = 74,667 number of insertions = 1,442 mapped reads with insertion percentage = 5.22% number of deletions = 5,091 mapped reads with deletion percentage = 23.15% homopolymer indels = 33.9% >>>>>>> Coverage mean coverageData = 0.0007X std coverageData = 0.7588X There is a 0.01% of reference with a coverageData >= 1X There is a 0% 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 65962 2.646412664303853E-4 0.3366906128814477 chr2 243199373 662101 0.002722461788583641 2.5566017046112464 chr3 198022430 34894 1.7621236139764572E-4 0.045488513713100455 chr4 191154276 21526 1.1261061196454742E-4 0.027650841383445472 chr5 180915260 26643 1.4726784241417777E-4 0.043080830848954504 chr6 171115067 37580 2.196182993049934E-4 0.07735579832188123 chr7 159138663 58289 3.6627805525801105E-4 0.18916632978252 chr8 146364022 67238 4.593888517220441E-4 0.2722423089461789 chr9 141213431 9708 6.874700183440766E-5 0.017777164962431088 chr10 135534747 44250 3.264845434802044E-4 0.45541135978258407 chr11 135006516 27738 2.0545674995420222E-4 0.051561553444953806 chr12 133851895 28948 2.1626888435161864E-4 0.060631217265618736 chr13 115169878 9897 8.593392796682479E-5 0.025845307149035476 chr14 107349540 15358 1.43065354541808E-4 0.058377982880129194 chr15 102531392 22883 2.2318042848769673E-4 0.06408158286224658 chr16 90354753 19750 2.1858285639937502E-4 0.06907925312772413 chr17 81195210 31951 3.935084347955994E-4 0.11204874729331252 chr18 78077248 10115 1.295511850007828E-4 0.03649250385233821 chr19 59128983 13989 2.36584485141576E-4 0.056055739731710554 chr20 63025520 41011 6.507046669349178E-4 0.23091654978134468 chr21 48129895 2895 6.0149726069421095E-5 0.016865832769231336 chr22 51304566 3048 5.940991684833666E-5 0.012851732694502892 chrMT 16571 150 0.009051958240299317 0.09471019106894038 chrX 155270560 1037753 0.006683514247646173 0.8456214433250959 chrY 59373566 5869 9.884870314173146E-5 0.025122967460632726