BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3083629.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 = 1,435,056 number of mapped reads = 1,296,750 (90.36%) number of supplementary alignments = 14,182 (0.99%) number of secondary alignments = 0 number of mapped bases = 86,402,361 bp number of sequenced bases = 86,373,400 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 48,152 duplication rate = 2.13% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.1529 >>>>>>> ACTG content number of A's = 23,570,218 bp (27.29%) number of C's = 16,585,876 bp (19.2%) number of T's = 25,729,090 bp (29.79%) number of G's = 20,484,228 bp (23.72%) number of N's = 3,988 bp (0%) GC percentage = 42.92% >>>>>>> Mismatches and indels general error rate = 0.0076 number of mismatches = 643,654 number of insertions = 7,702 mapped reads with insertion percentage = 0.59% number of deletions = 17,850 mapped reads with deletion percentage = 1.36% homopolymer indels = 42.89% >>>>>>> Coverage mean coverageData = 0.0279X std coverageData = 0.4783X There is a 2.53% of reference with a coverageData >= 1X There is a 0.15% of reference with a coverageData >= 2X There is a 0.02% 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 9256240 0.03713627658323868 1.220578530497232 chr2 243199373 7389990 0.03038655037979888 0.4934938496531574 chr3 198022430 6862231 0.03465380664200515 0.20040386722447756 chr4 191154276 3888898 0.020344289865637116 0.17674732091423542 chr5 180915260 4048836 0.022379737342223094 0.16226873600500502 chr6 171115067 5685868 0.03322833050113582 0.27029642812321925 chr7 159138663 6185890 0.03887106931393536 0.7802879946911685 chr8 146364022 5663257 0.03869295830091359 0.33923765146407125 chr9 141213431 3452641 0.02444980605279678 0.29098678738292433 chr10 135534747 3945442 0.02911018825305366 0.3048611977899559 chr11 135006516 3171918 0.02349455488503977 0.28765216411179884 chr12 133851895 3035766 0.022680037514597757 0.16294742356532746 chr13 115169878 2452054 0.02129075798795237 0.15381772919251965 chr14 107349540 1843474 0.017172630641919845 0.1559338420180409 chr15 102531392 2161982 0.021086049431573113 0.16995450681631932 chr16 90354753 2524141 0.027935896189102527 0.1973346514593134 chr17 81195210 1975977 0.024336127709996686 0.18211273962928914 chr18 78077248 2405763 0.03081259984983077 0.6179194022203826 chr19 59128983 2719742 0.04599676608677677 0.804710325778542 chr20 63025520 1819749 0.028873208820807825 0.18866328084690992 chr21 48129895 1285352 0.02670589661581435 0.17832456193540666 chr22 51304566 695415 0.013554641510854998 0.12116035400934598 chrMT 16571 7863 0.4745036509564903 0.8297151197869541 chrX 155270560 3745097 0.02411981382690962 0.19243459629027507 chrY 59373566 178775 0.003011020089310452 0.07265273380405396