BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3080645.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 = 1,410,298 number of mapped reads = 1,266,208 (89.78%) number of supplementary alignments = 10,558 (0.75%) number of secondary alignments = 0 number of mapped bases = 83,603,649 bp number of sequenced bases = 83,572,313 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 44,069 duplication rate = 3.03% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.2262 >>>>>>> ACTG content number of A's = 22,403,256 bp (26.81%) number of C's = 15,611,471 bp (18.68%) number of T's = 26,226,171 bp (31.38%) number of G's = 19,327,816 bp (23.13%) number of N's = 3,599 bp (0%) GC percentage = 41.81% >>>>>>> Mismatches and indels general error rate = 0.0069 number of mismatches = 566,050 number of insertions = 6,198 mapped reads with insertion percentage = 0.49% number of deletions = 19,515 mapped reads with deletion percentage = 1.53% homopolymer indels = 48.08% >>>>>>> Coverage mean coverageData = 0.027X std coverageData = 0.2209X There is a 2.36% of reference with a coverageData >= 1X There is a 0.27% of reference with a coverageData >= 2X There is a 0.04% 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 10160286 0.04076333274210779 0.2516423348669754 chr2 243199373 5655062 0.023252781988052248 0.34638618692555767 chr3 198022430 5301748 0.026773472075865345 0.18142076272956703 chr4 191154276 3624733 0.018962343275020433 0.15436292164071588 chr5 180915260 3654114 0.020197931340894072 0.15788684688672175 chr6 171115067 5007431 0.0292635306042337 0.22460507139735414 chr7 159138663 5269207 0.033110790933313296 0.3452663477017656 chr8 146364022 9894722 0.06760351256267062 0.3156815975727306 chr9 141213431 2649958 0.018765622938514963 0.170422045387814 chr10 135534747 3852762 0.028426378366279755 0.19658044466009184 chr11 135006516 3488594 0.025840189817208526 0.1919083900371418 chr12 133851895 2744408 0.020503318238415676 0.15925758477428298 chr13 115169878 1743009 0.01513424369521343 0.1372371729906635 chr14 107349540 1605474 0.014955574099339411 0.13848923006905844 chr15 102531392 1513619 0.014762493422502252 0.14226379375293838 chr16 90354753 2178112 0.024106224937607876 0.17580865982443827 chr17 81195210 1402305 0.017270784816000844 0.148454221700016 chr18 78077248 2566909 0.03287653017688329 0.23781561161884462 chr19 59128983 1332537 0.022536105516984793 0.18231866111238473 chr20 63025520 2218678 0.03520285116251322 0.21206451322676914 chr21 48129895 1187998 0.024683162097070853 0.17716230150586113 chr22 51304566 803940 0.01566995031202486 0.13856007582019295 chrMT 16571 17375 1.0485184961680043 1.176692213199486 chrX 155270560 5560632 0.035812532652680584 0.2168557538568082 chrY 59373566 170036 0.0028638333766242033 0.0607600894850737