BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472394.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 = 18,446,242 number of mapped reads = 18,272,647 (99.06%) number of supplementary alignments = 68,819 (0.37%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 9,164,361 number of mapped paired reads (second in pair) = 9,108,286 number of mapped paired reads (both in pair) = 18,161,200 number of mapped paired reads (singletons) = 111,447 number of mapped bases = 1,793,286,988 bp number of sequenced bases = 1,793,069,958 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 11,180,018 duplication rate = 47.47% >>>>>>> Insert size mean insert size = 18,295.3064 std insert size = 1,324,397.79 median insert size = 220 >>>>>>> Mapping quality mean mapping quality = 54.857 >>>>>>> ACTG content number of A's = 483,471,503 bp (26.96%) number of C's = 414,454,819 bp (23.11%) number of T's = 483,208,701 bp (26.95%) number of G's = 411,711,888 bp (22.96%) number of N's = 223,047 bp (0.01%) GC percentage = 46.08% >>>>>>> Mismatches and indels general error rate = 0.0059 number of mismatches = 10,472,943 number of insertions = 104,156 mapped reads with insertion percentage = 0.56% number of deletions = 90,843 mapped reads with deletion percentage = 0.49% homopolymer indels = 45.62% >>>>>>> Coverage mean coverageData = 0.5793X std coverageData = 16.0124X There is a 4.91% of reference with a coverageData >= 1X There is a 2.05% of reference with a coverageData >= 2X There is a 0.88% of reference with a coverageData >= 3X There is a 0.67% of reference with a coverageData >= 4X There is a 0.52% of reference with a coverageData >= 5X There is a 0.48% of reference with a coverageData >= 6X There is a 0.44% of reference with a coverageData >= 7X There is a 0.42% of reference with a coverageData >= 8X There is a 0.41% of reference with a coverageData >= 9X There is a 0.39% of reference with a coverageData >= 10X There is a 0.38% of reference with a coverageData >= 11X There is a 0.37% of reference with a coverageData >= 12X There is a 0.36% of reference with a coverageData >= 13X There is a 0.35% of reference with a coverageData >= 14X There is a 0.34% of reference with a coverageData >= 15X There is a 0.33% of reference with a coverageData >= 16X There is a 0.33% of reference with a coverageData >= 17X There is a 0.32% of reference with a coverageData >= 18X There is a 0.31% of reference with a coverageData >= 19X There is a 0.31% of reference with a coverageData >= 20X There is a 0.3% of reference with a coverageData >= 21X There is a 0.3% of reference with a coverageData >= 22X There is a 0.29% of reference with a coverageData >= 23X There is a 0.29% of reference with a coverageData >= 24X There is a 0.28% of reference with a coverageData >= 25X There is a 0.28% of reference with a coverageData >= 26X There is a 0.27% of reference with a coverageData >= 27X There is a 0.27% of reference with a coverageData >= 28X There is a 0.26% of reference with a coverageData >= 29X There is a 0.26% of reference with a coverageData >= 30X There is a 0.26% of reference with a coverageData >= 31X There is a 0.25% of reference with a coverageData >= 32X There is a 0.25% of reference with a coverageData >= 33X There is a 0.24% of reference with a coverageData >= 34X There is a 0.24% of reference with a coverageData >= 35X There is a 0.24% of reference with a coverageData >= 36X There is a 0.23% of reference with a coverageData >= 37X There is a 0.23% of reference with a coverageData >= 38X There is a 0.23% of reference with a coverageData >= 39X There is a 0.23% of reference with a coverageData >= 40X There is a 0.22% of reference with a coverageData >= 41X There is a 0.22% of reference with a coverageData >= 42X There is a 0.22% of reference with a coverageData >= 43X There is a 0.21% of reference with a coverageData >= 44X There is a 0.21% of reference with a coverageData >= 45X There is a 0.21% of reference with a coverageData >= 46X There is a 0.21% of reference with a coverageData >= 47X There is a 0.21% of reference with a coverageData >= 48X There is a 0.2% of reference with a coverageData >= 49X There is a 0.2% of reference with a coverageData >= 50X There is a 0.2% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 192915256 0.7739810445647797 19.220877755129692 chr2 243199373 157349256 0.6469969640916796 18.449710743755944 chr3 198022430 131540758 0.6642720120139926 14.796524416486934 chr4 191154276 48210715 0.2522084046919254 8.531260172979282 chr5 180915260 71738318 0.39652994446129086 13.746864610286657 chr6 171115067 155268178 0.9073904520634644 22.379246791065874 chr7 159138663 138329302 0.86923755291321 21.08177846331927 chr8 146364022 92819383 0.6341680266206404 16.1418909142546 chr9 141213431 63364886 0.4487171337123025 10.547858471773548 chr10 135534747 55417996 0.4088840480146394 11.718888585720016 chr11 135006516 60630227 0.4490911164613714 15.479042327593362 chr12 133851895 90563905 0.6765978546661592 15.94761948981619 chr13 115169878 54366456 0.4720544724376629 14.017721403276113 chr14 107349540 30361009 0.28282383883526657 8.357707416918856 chr15 102531392 30789444 0.3002928507983194 9.698439975840538 chr16 90354753 83981979 0.929469410424928 20.299250974418257 chr17 81195210 74274719 0.9147672504326302 18.72921609347822 chr18 78077248 18117712 0.23204854761274374 6.49404003198856 chr19 59128983 34662857 0.5862244747216437 11.690509575616785 chr20 63025520 66364520 1.0529785394868618 25.536486714935474 chr21 48129895 11637503 0.24179365028741492 10.964678857850256 chr22 51304566 16264567 0.3170198730459975 10.583258786034952 chrMT 16571 30498 1.8404441494176573 1.6650296568316938 chrX 155270560 114000172 0.7342033930965406 20.054909219973776 chrY 59373566 287372 0.0048400663689292306 0.31088553444356354