BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818950.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.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 = 3,377,841 number of mapped reads = 3,325,062 (98.44%) number of supplementary alignments = 45,545 (1.35%) number of secondary alignments = 0 number of mapped bases = 307,370,980 bp number of sequenced bases = 307,197,280 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,769,244 duplication rate = 42.01% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.1549 >>>>>>> ACTG content number of A's = 89,494,628 bp (29.13%) number of C's = 66,556,602 bp (21.67%) number of T's = 86,428,423 bp (28.13%) number of G's = 64,703,015 bp (21.06%) number of N's = 14,612 bp (0%) GC percentage = 42.73% >>>>>>> Mismatches and indels general error rate = 0.0069 number of mismatches = 2,030,154 number of insertions = 36,943 mapped reads with insertion percentage = 1.07% number of deletions = 94,408 mapped reads with deletion percentage = 2.78% homopolymer indels = 43.35% >>>>>>> Coverage mean coverageData = 0.0993X std coverageData = 1.1294X There is a 3.61% of reference with a coverageData >= 1X There is a 2% of reference with a coverageData >= 2X There is a 1.27% of reference with a coverageData >= 3X There is a 0.85% of reference with a coverageData >= 4X There is a 0.57% of reference with a coverageData >= 5X There is a 0.4% of reference with a coverageData >= 6X There is a 0.28% of reference with a coverageData >= 7X There is a 0.2% of reference with a coverageData >= 8X There is a 0.14% of reference with a coverageData >= 9X There is a 0.1% of reference with a coverageData >= 10X There is a 0.07% of reference with a coverageData >= 11X There is a 0.06% of reference with a coverageData >= 12X There is a 0.04% of reference with a coverageData >= 13X There is a 0.03% of reference with a coverageData >= 14X There is a 0.02% of reference with a coverageData >= 15X There is a 0.02% of reference with a coverageData >= 16X There is a 0.02% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% 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 36085120 0.14477444371141607 1.958469990876444 chr2 243199373 27200977 0.1118464108869228 1.7248347103713992 chr3 198022430 20469414 0.10336916883607579 0.7179219700863478 chr4 191154276 20102499 0.10516374219115035 0.8195724575955817 chr5 180915260 15874095 0.08774326167952885 0.6878360390513336 chr6 171115067 16386367 0.09576226855581338 0.764996102320549 chr7 159138663 15692623 0.09860974513779848 0.9301552345934446 chr8 146364022 19954905 0.13633750102877057 0.9644162414573638 chr9 141213431 11650893 0.08250555855412932 1.279305722990304 chr10 135534747 15038645 0.1109578564380985 1.3514177445913473 chr11 135006516 11803777 0.08743116517427944 0.795239252769355 chr12 133851895 13979969 0.10444356428424117 0.7508893261774695 chr13 115169878 4964043 0.04310192114643032 0.45357649533047384 chr14 107349540 7343712 0.06840934763204388 0.658152033284858 chr15 102531392 8956948 0.08735810394537509 0.6659385888383995 chr16 90354753 9295638 0.10287934714402905 1.2973098793222044 chr17 81195210 6557396 0.08076087247018636 0.7187249987371832 chr18 78077248 7699776 0.09861741028577237 1.598508385670719 chr19 59128983 4794714 0.08108906591544117 1.595601977081485 chr20 63025520 6720036 0.10662404689402007 0.7917930802933886 chr21 48129895 4169784 0.08663605021369775 0.7579878693758068 chr22 51304566 3788648 0.0738462147794019 0.6881452136272607 chrMT 16571 80518 4.858970490616136 5.233643096537866 chrX 155270560 17770261 0.11444707225890086 0.8848508607892265 chrY 59373566 990222 0.01667782595372493 1.037629236769855