BamQC report ----------------------------------- >>>>>>> Input bam file = SRR536751.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP014781/SRP014781.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 = 24,013,773 number of mapped reads = 23,167,785 (96.48%) number of supplementary alignments = 516 (0%) number of secondary alignments = 0 number of mapped bases = 1,155,324,119 bp number of sequenced bases = 1,155,222,216 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 213,507 duplication rate = 0.91% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.5781 >>>>>>> ACTG content number of A's = 361,140,662 bp (31.26%) number of C's = 215,257,695 bp (18.63%) number of T's = 359,308,759 bp (31.1%) number of G's = 219,055,320 bp (18.96%) number of N's = 459,780 bp (0.04%) GC percentage = 37.6% >>>>>>> Mismatches and indels general error rate = 0.0035 number of mismatches = 3,985,945 number of insertions = 64,159 mapped reads with insertion percentage = 0.28% number of deletions = 61,438 mapped reads with deletion percentage = 0.26% homopolymer indels = 48.26% >>>>>>> Coverage mean coverageData = 0.3732X std coverageData = 0.6829X There is a 28.31% of reference with a coverageData >= 1X There is a 7.06% of reference with a coverageData >= 2X There is a 1.55% of reference with a coverageData >= 3X There is a 0.32% of reference with a coverageData >= 4X There is a 0.06% 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 88140052 0.3536201901779815 0.6810909746030992 chr2 243199373 107030651 0.4400942719535712 0.7257967445064821 chr3 198022430 89885860 0.45391756883298523 0.7321660273280384 chr4 191154276 97913339 0.5122215471653901 0.7763351619650982 chr5 180915260 83311641 0.46050090523043774 0.7389878127703758 chr6 171115067 78775225 0.46036404847972856 0.7425187816198372 chr7 159138663 66443201 0.41751765251414735 0.7184764597335076 chr8 146364022 64603723 0.44139073330466416 0.7261294151685597 chr9 141213431 47949699 0.3395548048117321 0.6586801463567798 chr10 135534747 48941686 0.3611006556126895 0.6563810398075774 chr11 135006516 51319349 0.3801249785602941 0.6915776216457965 chr12 133851895 53430239 0.39917431874983916 0.7022779325957765 chr13 115169878 49471554 0.42955289055702567 0.7347118939694297 chr14 107349540 36797944 0.34278622898616984 0.6617091426984483 chr15 102531392 30642675 0.2988613965174685 0.6208907732379632 chr16 90354753 20266170 0.22429556085444669 0.529862504177588 chr17 81195210 17934045 0.2208756526401003 0.5344772993341397 chr18 78077248 35139742 0.45006378810892517 0.7339069899364997 chr19 59128983 7701294 0.13024566987732564 0.3935890948336891 chr20 63025520 17137643 0.27191593183205787 0.5841881436075715 chr21 48129895 14994905 0.31155075239619784 0.6537883236111142 chr22 51304566 5536870 0.10792158343177487 0.36478955663958645 chrMT 16571 977 0.05895842133848289 0.2436072551073781 chrX 155270560 36734395 0.2365831294741257 0.5128727263486678 chrY 59373566 5221240 0.08793879754502197 0.33383952398613126