BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1708591.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP051114/SRP051114.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 = 2,874,348 number of mapped reads = 2,810,739 (97.79%) number of supplementary alignments = 89 (0%) number of secondary alignments = 0 number of mapped bases = 140,192,660 bp number of sequenced bases = 140,180,443 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 26,588 duplication rate = 0.95% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.7092 >>>>>>> ACTG content number of A's = 43,445,918 bp (30.99%) number of C's = 26,547,584 bp (18.94%) number of T's = 43,244,615 bp (30.85%) number of G's = 26,937,523 bp (19.22%) number of N's = 4,803 bp (0%) GC percentage = 38.15% >>>>>>> Mismatches and indels general error rate = 0.0016 number of mismatches = 206,940 number of insertions = 8,877 mapped reads with insertion percentage = 0.32% number of deletions = 7,213 mapped reads with deletion percentage = 0.26% homopolymer indels = 49.07% >>>>>>> Coverage mean coverageData = 0.0453X std coverageData = 0.2188X There is a 4.31% of reference with a coverageData >= 1X There is a 0.21% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0% 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 10886869 0.043678402710980606 0.21557343706481746 chr2 243199373 12506403 0.05142448701954507 0.23246478617956337 chr3 198022430 10746127 0.05426722114257461 0.23870917836968678 chr4 191154276 11106198 0.058100703957048805 0.2471300884299166 chr5 180915260 9943734 0.05496348953648244 0.24008074889052647 chr6 171115067 9274871 0.054202538459106 0.2385933066910678 chr7 159138663 7772021 0.048838043838535954 0.22709563519463108 chr8 146364022 7738496 0.05287157249614253 0.23567030497776867 chr9 141213431 5759641 0.04078677898563345 0.20786871570697202 chr10 135534747 5995671 0.04423715049248589 0.21573138568017966 chr11 135006516 6195451 0.045890014671588146 0.22042594087706677 chr12 133851895 6293082 0.04701526265279995 0.2224974969170476 chr13 115169878 5331196 0.0462898467253738 0.22095563296463355 chr14 107349540 4336750 0.04039840319762898 0.20690983351694137 chr15 102531392 3650786 0.035606519416024315 0.194572870311435 chr16 90354753 2666710 0.029513776657659613 0.1766980115852483 chr17 81195210 2264467 0.027889169816790918 0.17153869177679507 chr18 78077248 4029645 0.05161100196564305 0.23304921711612053 chr19 59128983 1118432 0.01891512323152928 0.140720026496059 chr20 63025520 2025595 0.0321392826271009 0.1841385803646648 chr21 48129895 1640156 0.03407769744770896 0.190687751208918 chr22 51304566 745614 0.014533092434696748 0.12353162444477521 chrMT 16571 150 0.009051958240299317 0.09471019106894038 chrX 155270560 7983282 0.051415297272064966 0.2327374145637959 chrY 59373566 181313 0.003053766384858878 0.05654487371462251