BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818932.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.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 = 668,107 number of mapped reads = 658,892 (98.62%) number of supplementary alignments = 7,774 (1.16%) number of secondary alignments = 0 number of mapped bases = 61,099,254 bp number of sequenced bases = 61,066,720 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 155,975 duplication rate = 20.83% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.2972 >>>>>>> ACTG content number of A's = 17,089,903 bp (27.99%) number of C's = 13,189,920 bp (21.6%) number of T's = 17,159,526 bp (28.1%) number of G's = 13,624,790 bp (22.31%) number of N's = 2,581 bp (0%) GC percentage = 43.91% >>>>>>> Mismatches and indels general error rate = 0.0065 number of mismatches = 381,741 number of insertions = 6,647 mapped reads with insertion percentage = 0.98% number of deletions = 18,139 mapped reads with deletion percentage = 2.69% homopolymer indels = 42.76% >>>>>>> Coverage mean coverageData = 0.0197X std coverageData = 0.2466X There is a 1.36% of reference with a coverageData >= 1X There is a 0.38% of reference with a coverageData >= 2X There is a 0.12% of reference with a coverageData >= 3X There is a 0.04% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.01% 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 7229779 0.029006062135347697 0.3889881638876921 chr2 243199373 5399944 0.0222037743493689 0.3194010017749001 chr3 198022430 4030781 0.020355173906309504 0.19543285006890418 chr4 191154276 3947803 0.020652444102270566 0.2050524428351561 chr5 180915260 3153970 0.017433410537065805 0.18314439160252322 chr6 171115067 3236525 0.018914319216553854 0.19775507994466582 chr7 159138663 3062271 0.019242784514282366 0.22462098699238717 chr8 146364022 3952563 0.02700501766752488 0.23972371512036977 chr9 141213431 2265246 0.016041292842746666 0.26191121120698757 chr10 135534747 2982985 0.022009005557814633 0.28308989978178734 chr11 135006516 2319260 0.017178874536692732 0.19406144931451438 chr12 133851895 2717408 0.020301602752803762 0.1986277017455172 chr13 115169878 982673 0.008532378579058668 0.12528908719378953 chr14 107349540 1494130 0.01391836425195674 0.16945044251347507 chr15 102531392 1814431 0.01769634611027226 0.18315880113334235 chr16 90354753 1862455 0.020612695383053065 0.26911889352313595 chr17 81195210 1340242 0.016506417065735773 0.1847057356692963 chr18 78077248 1561632 0.02000111479339026 0.33646030892233236 chr19 59128983 974329 0.016478027366038074 0.31442501920054833 chr20 63025520 1347472 0.021379783935142463 0.2087899020713945 chr21 48129895 816021 0.016954555998927485 0.18500687302035967 chr22 51304566 744298 0.014507441696319973 0.17228478655074253 chrMT 16571 146903 8.86506547583127 6.783450139617809 chrX 155270560 3536122 0.022773937313036032 0.2255777366777632 chrY 59373566 180011 0.0030318374341874632 0.1707550416541701