BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3083621.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 = 1,405,304 number of mapped reads = 1,289,066 (91.73%) number of supplementary alignments = 14,951 (1.06%) number of secondary alignments = 0 number of mapped bases = 86,316,847 bp number of sequenced bases = 86,284,150 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 55,873 duplication rate = 3.7% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.8972 >>>>>>> ACTG content number of A's = 23,831,833 bp (27.62%) number of C's = 15,835,294 bp (18.35%) number of T's = 27,513,553 bp (31.89%) number of G's = 19,098,771 bp (22.13%) number of N's = 4,699 bp (0.01%) GC percentage = 40.49% >>>>>>> Mismatches and indels general error rate = 0.0074 number of mismatches = 625,709 number of insertions = 6,274 mapped reads with insertion percentage = 0.48% number of deletions = 20,124 mapped reads with deletion percentage = 1.55% homopolymer indels = 49.19% >>>>>>> Coverage mean coverageData = 0.0279X std coverageData = 0.2615X There is a 2.39% of reference with a coverageData >= 1X There is a 0.31% of reference with a coverageData >= 2X There is a 0.05% 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 9407681 0.03774386182973642 0.5100837540841038 chr2 243199373 7522929 0.030933175966699554 0.29995621707243136 chr3 198022430 7330613 0.03701910435095661 0.2211155390636604 chr4 191154276 3724293 0.01948317912595374 0.16262663882656445 chr5 180915260 3946382 0.021813428010439805 0.16781854987991718 chr6 171115067 6298399 0.03680797436733026 0.23982961209776404 chr7 159138663 6872262 0.04318411296442776 0.39316903080475474 chr8 146364022 6758390 0.04617521374207659 0.32831113946879603 chr9 141213431 3617095 0.025614383662981747 0.19806115789588236 chr10 135534747 3524135 0.02600170862457876 0.20958317923332312 chr11 135006516 3003967 0.022250533448326303 0.1879667643772066 chr12 133851895 3423493 0.025576724184592232 0.18135053708017623 chr13 115169878 2886095 0.025059460425928385 0.18049588880017664 chr14 107349540 1648929 0.015360373225632825 0.1433414611639925 chr15 102531392 2083882 0.02032433149839612 0.16690191050760242 chr16 90354753 2053427 0.022726275395827823 0.17419350615876614 chr17 81195210 1594718 0.01964054283497758 0.16212274082024408 chr18 78077248 2044504 0.026185656543632276 0.27272940339475144 chr19 59128983 2250880 0.03806728757705845 0.31798702584475386 chr20 63025520 1701747 0.027000919627477884 0.18826058174529633 chr21 48129895 1494509 0.031051574078854734 0.20258636775521402 chr22 51304566 504064 0.00982493449023621 0.1113508747935908 chrMT 16571 2734 0.16498702552652222 0.4640816331723681 chrX 155270560 2469011 0.015901346655798756 0.1470136820425325 chrY 59373566 152708 0.0025719863280571696 0.06309835386163222