BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472521.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 16,597,032 number of mapped reads = 16,398,086 (98.8%) number of supplementary alignments = 63,914 (0.39%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 8,231,091 number of mapped paired reads (second in pair) = 8,166,995 number of mapped paired reads (both in pair) = 16,288,806 number of mapped paired reads (singletons) = 109,280 number of mapped bases = 1,615,377,554 bp number of sequenced bases = 1,615,163,552 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 10,526,597 duplication rate = 45.33% >>>>>>> Insert size mean insert size = 23,542.1047 std insert size = 1,518,106.5747 median insert size = 240 >>>>>>> Mapping quality mean mapping quality = 55.1988 >>>>>>> ACTG content number of A's = 447,493,544 bp (27.71%) number of C's = 362,118,470 bp (22.42%) number of T's = 445,871,180 bp (27.61%) number of G's = 359,432,048 bp (22.25%) number of N's = 248,310 bp (0.02%) GC percentage = 44.67% >>>>>>> Mismatches and indels general error rate = 0.0064 number of mismatches = 10,127,590 number of insertions = 90,473 mapped reads with insertion percentage = 0.55% number of deletions = 78,499 mapped reads with deletion percentage = 0.47% homopolymer indels = 45.74% >>>>>>> Coverage mean coverageData = 0.5218X std coverageData = 20.5415X There is a 5% of reference with a coverageData >= 1X There is a 2.26% of reference with a coverageData >= 2X There is a 1.03% of reference with a coverageData >= 3X There is a 0.71% of reference with a coverageData >= 4X There is a 0.51% of reference with a coverageData >= 5X There is a 0.43% of reference with a coverageData >= 6X There is a 0.38% of reference with a coverageData >= 7X There is a 0.35% of reference with a coverageData >= 8X There is a 0.33% of reference with a coverageData >= 9X There is a 0.31% of reference with a coverageData >= 10X There is a 0.3% of reference with a coverageData >= 11X There is a 0.29% of reference with a coverageData >= 12X There is a 0.28% of reference with a coverageData >= 13X There is a 0.27% of reference with a coverageData >= 14X There is a 0.26% of reference with a coverageData >= 15X There is a 0.25% of reference with a coverageData >= 16X There is a 0.25% of reference with a coverageData >= 17X There is a 0.24% of reference with a coverageData >= 18X There is a 0.24% of reference with a coverageData >= 19X There is a 0.23% of reference with a coverageData >= 20X There is a 0.22% of reference with a coverageData >= 21X There is a 0.22% of reference with a coverageData >= 22X There is a 0.22% of reference with a coverageData >= 23X There is a 0.21% of reference with a coverageData >= 24X There is a 0.21% of reference with a coverageData >= 25X There is a 0.2% of reference with a coverageData >= 26X There is a 0.2% of reference with a coverageData >= 27X There is a 0.2% of reference with a coverageData >= 28X There is a 0.19% of reference with a coverageData >= 29X There is a 0.19% of reference with a coverageData >= 30X There is a 0.19% of reference with a coverageData >= 31X There is a 0.18% of reference with a coverageData >= 32X There is a 0.18% of reference with a coverageData >= 33X There is a 0.18% of reference with a coverageData >= 34X There is a 0.17% of reference with a coverageData >= 35X There is a 0.17% of reference with a coverageData >= 36X There is a 0.17% of reference with a coverageData >= 37X There is a 0.17% of reference with a coverageData >= 38X There is a 0.16% of reference with a coverageData >= 39X There is a 0.16% of reference with a coverageData >= 40X There is a 0.16% of reference with a coverageData >= 41X There is a 0.16% of reference with a coverageData >= 42X There is a 0.16% of reference with a coverageData >= 43X There is a 0.15% of reference with a coverageData >= 44X There is a 0.15% of reference with a coverageData >= 45X There is a 0.15% of reference with a coverageData >= 46X There is a 0.15% of reference with a coverageData >= 47X There is a 0.15% of reference with a coverageData >= 48X There is a 0.14% of reference with a coverageData >= 49X There is a 0.14% of reference with a coverageData >= 50X There is a 0.14% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 137078181 0.5499612416211392 23.040202425455607 chr2 243199373 116221262 0.47788471066494076 22.28256869095099 chr3 198022430 183482069 0.9265721514476921 27.613943710521877 chr4 191154276 50030456 0.26172815511592323 9.17616624548075 chr5 180915260 106863049 0.5906801283650699 22.626966504121906 chr6 171115067 117855545 0.6887502489771985 23.56940680561766 chr7 159138663 62285821 0.39139339130931367 12.856452369012361 chr8 146364022 78995758 0.5397211481384407 23.221176236697406 chr9 141213431 103165965 0.7305676540073586 26.375769422481454 chr10 135534747 35784996 0.2640282052542585 10.557615315151688 chr11 135006516 72828138 0.5394416518384935 20.16183762961907 chr12 133851895 64661278 0.4830807811872966 14.639371192015052 chr13 115169878 31936747 0.2773012141247558 12.788772353180562 chr14 107349540 33199257 0.3092631510111734 10.12218078455758 chr15 102531392 56420523 0.550275597545774 22.03503496768693 chr16 90354753 59416703 0.657593552383459 22.085592058702833 chr17 81195210 85188087 1.0491762629839865 28.173460523108762 chr18 78077248 32523932 0.41656094231190116 19.56649128865799 chr19 59128983 54814990 0.9270409741361525 42.42576272577499 chr20 63025520 30477304 0.48357084558762864 16.423543688537766 chr21 48129895 8827299 0.18340573982137298 9.560749716750912 chr22 51304566 15442691 0.30100032422065515 11.367108416450009 chrMT 16571 1669 0.10071812202039708 0.3574176228036012 chrX 155270560 74993178 0.4829838831005697 16.68607015468133 chrY 59373566 2882656 0.048551168376849724 2.585633504538595