BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3124795.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP068920/SRP068920.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 = 322,295 number of mapped reads = 318,271 (98.75%) number of supplementary alignments = 108,935 (33.8%) number of secondary alignments = 0 number of mapped bases = 46,104,695 bp number of sequenced bases = 46,029,173 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 370,682 duplication rate = 1.42% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 51.0935 >>>>>>> ACTG content number of A's = 12,937,157 bp (28.11%) number of C's = 8,230,841 bp (17.88%) number of T's = 14,615,876 bp (31.75%) number of G's = 10,245,299 bp (22.26%) number of N's = 0 bp (0%) GC percentage = 40.14% >>>>>>> Mismatches and indels general error rate = 0.0097 number of mismatches = 442,017 number of insertions = 3,016 mapped reads with insertion percentage = 0.91% number of deletions = 67,352 mapped reads with deletion percentage = 20.92% homopolymer indels = 84.65% >>>>>>> Coverage mean coverageData = 0.0149X std coverageData = 29.9531X There is a 0.21% 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 3279075 0.01315573452472963 6.901355432723021 chr2 243199373 594004 0.0024424569548540734 0.14713489427896517 chr3 198022430 987289 0.004985743281708037 2.9944113458589046 chr4 191154276 2011738 0.010524159030583234 9.292674310288774 chr5 180915260 361170 0.001996349008922741 0.05083877375235198 chr6 171115067 392524 0.0022939183958593195 0.049732209631587414 chr7 159138663 510491 0.0032078376830399786 0.0656286073141814 chr8 146364022 5868725 0.04009677323570679 25.50155655263875 chr9 141213431 254956 0.0018054656571583477 0.04329204699844888 chr10 135534747 28697339 0.21173418355958565 139.86352381485275 chr11 135006516 242113 0.0017933430709374057 0.05924328361448744 chr12 133851895 327804 0.0024490052979825204 0.05433220935552297 chr13 115169878 392974 0.0034121248265974544 2.0037959560749057 chr14 107349540 230978 0.002151644059210687 0.0819646382905085 chr15 102531392 294620 0.002873461427306088 0.6983640760488874 chr16 90354753 218058 0.0024133539494042996 0.11756520190049999 chr17 81195210 242365 0.002984966724022267 0.4859254078531382 chr18 78077248 285183 0.0036525749473137166 1.7101190645016362 chr19 59128983 163193 0.0027599493804924737 0.1548983600325562 chr20 63025520 163495 0.0025941079105733676 0.07507041413457044 chr21 48129895 64069 0.0013311684972510329 0.040004430405834776 chr22 51304566 67057 0.001307037662105942 0.036743501842526116 chrMT 16571 18150 1.0952869470762174 1.1862285167263729 chrX 155270560 313042 0.0020161065948367802 0.04647450746870476 chrY 59373566 124283 0.002093237923422016 0.06812168176460079