BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3084287.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 = 2,676,256 number of mapped reads = 2,394,448 (89.47%) number of supplementary alignments = 18,311 (0.68%) number of secondary alignments = 0 number of mapped bases = 157,332,249 bp number of sequenced bases = 157,278,032 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 80,800 duplication rate = 2.72% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.0632 >>>>>>> ACTG content number of A's = 44,054,882 bp (28.01%) number of C's = 30,133,513 bp (19.16%) number of T's = 48,019,836 bp (30.53%) number of G's = 34,868,286 bp (22.17%) number of N's = 201,515 bp (0.13%) GC percentage = 41.33% >>>>>>> Mismatches and indels general error rate = 0.0106 number of mismatches = 1,648,932 number of insertions = 12,001 mapped reads with insertion percentage = 0.5% number of deletions = 33,768 mapped reads with deletion percentage = 1.4% homopolymer indels = 45.94% >>>>>>> Coverage mean coverageData = 0.0508X std coverageData = 0.3574X There is a 4.35% of reference with a coverageData >= 1X There is a 0.55% of reference with a coverageData >= 2X There is a 0.09% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% 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 15427885 0.06189707748009984 0.619732902860697 chr2 243199373 14766809 0.06071894354760528 0.4277143911720342 chr3 198022430 10702173 0.05404525638837984 0.2657256408569491 chr4 191154276 7602047 0.03976917053113685 0.23583954225453427 chr5 180915260 7796763 0.04309621532202425 0.23415463146708623 chr6 171115067 7693515 0.04496106120216754 0.2744758340189476 chr7 159138663 9183754 0.05770913131273448 0.480387047289241 chr8 146364022 7495355 0.051210365071820724 0.34258194346532067 chr9 141213431 5766286 0.040833835416122705 0.2972728775564459 chr10 135534747 11122519 0.08206396696191863 0.48188370726076635 chr11 135006516 8621894 0.06386279903704796 0.3466750004452981 chr12 133851895 5794249 0.04328850928856853 0.23645420414475624 chr13 115169878 4091424 0.035525122289354165 0.21227827037787383 chr14 107349540 4581210 0.04267563698922231 0.24089900216936388 chr15 102531392 3153733 0.03075870656276665 0.2074677313957582 chr16 90354753 3746141 0.04146036456986386 0.2552268617631076 chr17 81195210 4766152 0.05869991591868535 0.2936730362548255 chr18 78077248 4645513 0.059498933671432684 0.4972108194045214 chr19 59128983 3303553 0.05587028276809699 0.45878803477987945 chr20 63025520 3786932 0.06008569227195587 0.27893517607406154 chr21 48129895 1575241 0.032728951517554734 0.2137992027663773 chr22 51304566 1386514 0.027025157955726593 0.1847792494724903 chrMT 16571 5773 0.3483796994749864 0.6422456563157686 chrX 155270560 9968012 0.06419769465634696 0.31538994778740237 chrY 59373566 348802 0.005874701883326327 0.1164220541162592