BamQC report ----------------------------------- >>>>>>> Input bam file = ERR2094109.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/ERP024468/ERP024468.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 = 458,544 number of mapped reads = 438,470 (95.62%) number of supplementary alignments = 33,393 (7.28%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 220,429 number of mapped paired reads (second in pair) = 218,041 number of mapped paired reads (both in pair) = 434,930 number of mapped paired reads (singletons) = 3,540 number of mapped bases = 55,928,211 bp number of sequenced bases = 54,918,931 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 423,105 duplication rate = 53.17% >>>>>>> Insert size mean insert size = 1,753,434.971 std insert size = 11,583,689.6526 median insert size = 159 >>>>>>> Mapping quality mean mapping quality = 40.8988 >>>>>>> ACTG content number of A's = 15,809,380 bp (28.79%) number of C's = 11,769,314 bp (21.43%) number of T's = 14,907,055 bp (27.14%) number of G's = 12,432,485 bp (22.64%) number of N's = 697 bp (0%) GC percentage = 44.07% >>>>>>> Mismatches and indels general error rate = 0.0347 number of mismatches = 1,821,392 number of insertions = 37,613 mapped reads with insertion percentage = 8.45% number of deletions = 139,218 mapped reads with deletion percentage = 30.56% homopolymer indels = 28.69% >>>>>>> Coverage mean coverageData = 0.0181X std coverageData = 3.5842X There is a 0.02% of reference with a coverageData >= 1X There is a 0.01% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0.01% 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 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% 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 0.01% 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 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 1176330 0.004719466676875401 1.8628361952822416 chr2 243199373 2362482 0.009714178004891485 3.093059406313556 chr3 198022430 1339286 0.006763304540803787 2.326412223772383 chr4 191154276 2676476 0.01400165382646214 3.8743601802980754 chr5 180915260 943025 0.00521252325536276 1.6719945088344021 chr6 171115067 1158824 0.0067721914867964255 2.002796073553885 chr7 159138663 1184725 0.007444608228234267 2.2457436346310797 chr8 146364022 915612 0.006255717679034538 1.7651525841457438 chr9 141213431 919674 0.006512652468588487 2.565181218915447 chr10 135534747 1258987 0.009289034936553945 3.047679949732556 chr11 135006516 1653609 0.012248364367835402 3.0118473051604036 chr12 133851895 1807057 0.01350042149197813 3.4682225399846214 chr13 115169878 899612 0.007811174376689016 2.404304511495971 chr14 107349540 240916 0.0022442201429088565 0.7720606903947905 chr15 102531392 468824 0.004572492295822923 1.1661916987514012 chr16 90354753 190679 0.002110337239259566 0.7969519774213809 chr17 81195210 333682 0.004109626663937441 1.2408511133225375 chr18 78077248 334965 0.004290174264338825 0.9504286820143998 chr19 59128983 103885 0.0017569218127766546 0.5236110080026329 chr20 63025520 212841 0.003377060593867373 1.157110305409343 chr21 48129895 200381 0.004163337568054117 1.1296040135652732 chr22 51304566 54702 0.0010662208895793018 0.333245264761404 chrMT 16571 524174 31.632007724337697 138.91048278045122 chrX 155270560 34251384 0.22059161762538887 12.201846278480282 chrY 59373566 716079 0.01206056917652546 2.6366284117137657