BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3084386.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 1,665,810 number of mapped reads = 1,533,815 (92.08%) number of supplementary alignments = 7,818 (0.47%) number of secondary alignments = 0 number of mapped bases = 103,854,568 bp number of sequenced bases = 103,819,445 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 47,035 duplication rate = 2.58% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.7413 >>>>>>> ACTG content number of A's = 29,399,723 bp (28.32%) number of C's = 19,441,586 bp (18.73%) number of T's = 32,589,948 bp (31.39%) number of G's = 22,249,601 bp (21.43%) number of N's = 138,587 bp (0.13%) GC percentage = 40.16% >>>>>>> Mismatches and indels general error rate = 0.0099 number of mismatches = 1,014,556 number of insertions = 7,295 mapped reads with insertion percentage = 0.47% number of deletions = 20,491 mapped reads with deletion percentage = 1.32% homopolymer indels = 47.71% >>>>>>> Coverage mean coverageData = 0.0335X std coverageData = 0.2598X There is a 2.94% of reference with a coverageData >= 1X There is a 0.32% of reference with a coverageData >= 2X There is a 0.04% of reference with a coverageData >= 3X There is a 0.01% 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 10297791 0.041315006392702226 0.40541322989438533 chr2 243199373 10290383 0.0423125391856993 0.2925283449923951 chr3 198022430 7270493 0.03671550238021016 0.21445616388577451 chr4 191154276 5150529 0.02694435671425943 0.1894255000293621 chr5 180915260 5259231 0.029070134824447643 0.1885767324614116 chr6 171115067 5048073 0.029501043295036083 0.21038728014972466 chr7 159138663 5971290 0.037522559806852214 0.3466374968435928 chr8 146364022 4928936 0.03367587151984659 0.24475577620578923 chr9 141213431 3954335 0.028002541769557316 0.232775455529232 chr10 135534747 6772146 0.049966124185113946 0.3744336179987594 chr11 135006516 5851139 0.04333967850855436 0.2700525672600078 chr12 133851895 4076824 0.03045772344127067 0.19406332300148346 chr13 115169878 2683619 0.023301396568293664 0.1687058523278236 chr14 107349540 2855977 0.026604464257601847 0.18536178772033096 chr15 102531392 2291980 0.022353934295557012 0.16606625181432985 chr16 90354753 2255371 0.02496128786938303 0.1869549789977146 chr17 81195210 2857462 0.03519249472967679 0.21888648125578447 chr18 78077248 2878398 0.036866027859998346 0.35554116431748 chr19 59128983 2013752 0.03405693617290864 0.3010101429214813 chr20 63025520 2155909 0.034206921259832525 0.20589571939551746 chr21 48129895 1079545 0.022429822462733402 0.17376998489335116 chr22 51304566 830460 0.016186863368067475 0.13938098688658163 chrMT 16571 20011 1.2075915756441977 1.3867630512423919 chrX 155270560 6841592 0.044062390191675745 0.25152325331593023 chrY 59373566 219322 0.0036939334248510523 0.08653192547340396