BamQC report ----------------------------------- >>>>>>> Input bam file = SRR089577.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP002535/SRP002535.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 = 10,423,807 number of mapped reads = 8,985,115 (86.2%) number of supplementary alignments = 309 (0%) number of secondary alignments = 0 number of mapped bases = 422,211,676 bp number of sequenced bases = 422,128,347 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 941,430 duplication rate = 8.18% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.7372 >>>>>>> ACTG content number of A's = 122,429,125 bp (29%) number of C's = 89,513,499 bp (21.21%) number of T's = 120,100,971 bp (28.45%) number of G's = 90,072,554 bp (21.34%) number of N's = 12,198 bp (0%) GC percentage = 42.54% >>>>>>> Mismatches and indels general error rate = 0.0043 number of mismatches = 1,807,777 number of insertions = 16,235 mapped reads with insertion percentage = 0.18% number of deletions = 55,850 mapped reads with deletion percentage = 0.62% homopolymer indels = 44.53% >>>>>>> Coverage mean coverageData = 0.1364X std coverageData = 0.8433X There is a 8.27% of reference with a coverageData >= 1X There is a 2.78% of reference with a coverageData >= 2X There is a 1.17% of reference with a coverageData >= 3X There is a 0.56% of reference with a coverageData >= 4X There is a 0.29% of reference with a coverageData >= 5X There is a 0.16% of reference with a coverageData >= 6X There is a 0.09% of reference with a coverageData >= 7X There is a 0.06% of reference with a coverageData >= 8X There is a 0.04% of reference with a coverageData >= 9X There is a 0.02% of reference with a coverageData >= 10X There is a 0.02% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% 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 34172546 0.13710114688139532 1.138288437495469 chr2 243199373 35318181 0.1452231581205598 1.229482862314412 chr3 198022430 25462171 0.1285822570705753 0.5542759457450385 chr4 191154276 27378674 0.1432281535778985 0.6442383250846403 chr5 180915260 26911603 0.1487525319865223 0.6067598757981743 chr6 171115067 25735991 0.15040166509708933 0.7284985721745646 chr7 159138663 23533729 0.14788190723960024 1.1311071167004154 chr8 146364022 21576855 0.14741911779385236 0.9071936846799495 chr9 141213431 17439394 0.12349670903470931 0.7935925190668541 chr10 135534747 19821813 0.14624893939559278 0.8730957432078249 chr11 135006516 19926237 0.14759463165466769 0.8377193251680465 chr12 133851895 19304664 0.14422406197536464 0.6327239944447783 chr13 115169878 13926947 0.1209252561681102 0.5439422361951839 chr14 107349540 13558894 0.12630602795317056 0.7145697607920773 chr15 102531392 12009983 0.11713469178298096 0.5327074898173741 chr16 90354753 12207527 0.1351066390497465 0.6427133382747962 chr17 81195210 11097832 0.13668087070653553 0.661742430591954 chr18 78077248 10831262 0.13872494583825495 1.2614443182454027 chr19 59128983 8285060 0.1401184255105487 1.1159442693821502 chr20 63025520 9480019 0.15041556182321067 0.6639260614568334 chr21 48129895 5403291 0.11226475769373692 0.6422675872818642 chr22 51304566 4969857 0.09686968212536873 0.48755822225628453 chrMT 16571 126916 7.658922213505521 7.458420277421798 chrX 155270560 22516129 0.14501222253593984 0.7488325153489204 chrY 59373566 1216101 0.020482195729998768 0.4111504760848919