BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3084263.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 = 2,056,835 number of mapped reads = 1,723,307 (83.78%) number of supplementary alignments = 12,070 (0.59%) number of secondary alignments = 0 number of mapped bases = 110,253,131 bp number of sequenced bases = 110,215,614 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 52,128 duplication rate = 2.53% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.2517 >>>>>>> ACTG content number of A's = 32,097,464 bp (29.12%) number of C's = 20,642,398 bp (18.73%) number of T's = 33,546,339 bp (30.44%) number of G's = 23,928,214 bp (21.71%) number of N's = 1,199 bp (0%) GC percentage = 40.44% >>>>>>> Mismatches and indels general error rate = 0.0086 number of mismatches = 929,556 number of insertions = 8,659 mapped reads with insertion percentage = 0.5% number of deletions = 23,627 mapped reads with deletion percentage = 1.36% homopolymer indels = 46.28% >>>>>>> Coverage mean coverageData = 0.0356X std coverageData = 0.2577X There is a 3.16% of reference with a coverageData >= 1X There is a 0.31% 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 8754785 0.035124426029012785 0.34113256964751143 chr2 243199373 9368783 0.03852305573172674 0.3143641193507406 chr3 198022430 7440187 0.037572445707286795 0.2126724449423777 chr4 191154276 7392309 0.038671952072890065 0.22007615274610104 chr5 180915260 6788962 0.03752564598475552 0.21266861711935392 chr6 171115067 6557010 0.03831930241420529 0.24277147127671028 chr7 159138663 6122759 0.03847436496308883 0.2943165480790273 chr8 146364022 5584853 0.03815728020920332 0.2959975477433939 chr9 141213431 4566177 0.032335288277217766 0.24414309853293448 chr10 135534747 5125505 0.03781690757131085 0.26328404155272567 chr11 135006516 4865789 0.03604114189569932 0.23594240235090974 chr12 133851895 4901793 0.03662102056904013 0.2117662185410644 chr13 115169878 3712440 0.032234470197146516 0.19834722841717425 chr14 107349540 3342912 0.0311404408439943 0.20336147734143198 chr15 102531392 3080582 0.030045256773652308 0.19432864953882978 chr16 90354753 2987031 0.033058924968783876 0.21709999795074278 chr17 81195210 2774615 0.03417215128823486 0.2143486243666961 chr18 78077248 2952901 0.03782024950469566 0.4577226408364449 chr19 59128983 1933664 0.03270247350609768 0.2811450791664463 chr20 63025520 2069873 0.03284182343914021 0.20218168059433475 chr21 48129895 1427765 0.029664826819173404 0.19568052053768506 chr22 51304566 1131738 0.022059206192290955 0.1619006691084509 chrMT 16571 8560 0.5165650835797477 0.7605884041842855 chrX 155270560 7085687 0.04563445253240537 0.25028326613094054 chrY 59373566 276451 0.00465612929497952 0.09828030819133883