BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3082440.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 = 2,958,054 number of mapped reads = 2,679,940 (90.6%) number of supplementary alignments = 25,671 (0.87%) number of secondary alignments = 0 number of mapped bases = 182,311,053 bp number of sequenced bases = 182,245,031 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 103,844 duplication rate = 2.88% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.4844 >>>>>>> ACTG content number of A's = 51,752,112 bp (28.4%) number of C's = 34,193,697 bp (18.76%) number of T's = 56,746,344 bp (31.14%) number of G's = 39,549,152 bp (21.7%) number of N's = 3,726 bp (0%) GC percentage = 40.46% >>>>>>> Mismatches and indels general error rate = 0.0084 number of mismatches = 1,506,859 number of insertions = 14,560 mapped reads with insertion percentage = 0.54% number of deletions = 41,016 mapped reads with deletion percentage = 1.52% homopolymer indels = 47.67% >>>>>>> Coverage mean coverageData = 0.0589X std coverageData = 0.4877X There is a 5.1% of reference with a coverageData >= 1X There is a 0.58% of reference with a coverageData >= 2X There is a 0.08% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% 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 14166511 0.056836412054516006 0.8787204740513567 chr2 243199373 15647242 0.06433915436122445 0.5818716941930419 chr3 198022430 12501076 0.06312959597556701 0.27964690414699095 chr4 191154276 12287534 0.06428071742428614 0.2922161023863669 chr5 180915260 11537894 0.06377512875364964 0.28423077759228804 chr6 171115067 10780472 0.06300130192509582 0.3533257958406177 chr7 159138663 10120632 0.06359631160153709 0.6230227165992386 chr8 146364022 9545691 0.06521883499484593 0.8472993063754912 chr9 141213431 7607913 0.05387527904480984 0.43683118130686277 chr10 135534747 8421829 0.06213778522787223 0.4213813804796297 chr11 135006516 8286844 0.061381066970130536 0.3952647362229127 chr12 133851895 8236535 0.06153469101053818 0.2831063614772029 chr13 115169878 6040732 0.05245062428563135 0.2548995411198643 chr14 107349540 5547790 0.05167968116118616 0.2751843149712592 chr15 102531392 5142390 0.05015429810998762 0.25475420732055765 chr16 90354753 4822042 0.05336788425507621 0.29006605078136405 chr17 81195210 4512391 0.055574596087626355 0.297426685609062 chr18 78077248 5003318 0.06408163873808667 0.8262164144735308 chr19 59128983 3230523 0.05463518626728283 0.6379235163286447 chr20 63025520 3533660 0.05606712963256789 0.27068586594895755 chr21 48129895 2393820 0.049736655357340794 0.2693352416212617 chr22 51304566 1802283 0.035129095527286984 0.2063207498074514 chrMT 16571 7240 0.43690785106511376 0.7719456750043027 chrX 155270560 10695549 0.068883302797388 0.3386465099320635 chrY 59373566 439142 0.0073962544206962405 0.14539793261590994