BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3084286.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 = 2,470,618 number of mapped reads = 2,195,422 (88.86%) number of supplementary alignments = 13,805 (0.56%) number of secondary alignments = 0 number of mapped bases = 143,284,599 bp number of sequenced bases = 143,235,032 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 66,906 duplication rate = 2.44% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.2291 >>>>>>> ACTG content number of A's = 39,515,889 bp (27.59%) number of C's = 27,689,491 bp (19.33%) number of T's = 43,168,153 bp (30.14%) number of G's = 32,679,602 bp (22.82%) number of N's = 181,897 bp (0.13%) GC percentage = 42.15% >>>>>>> Mismatches and indels general error rate = 0.0106 number of mismatches = 1,497,369 number of insertions = 11,162 mapped reads with insertion percentage = 0.5% number of deletions = 30,852 mapped reads with deletion percentage = 1.39% homopolymer indels = 45.98% >>>>>>> Coverage mean coverageData = 0.0463X std coverageData = 0.327X There is a 4.01% of reference with a coverageData >= 1X There is a 0.46% of reference with a coverageData >= 2X There is a 0.08% 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% 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 13765359 0.05522697975544864 0.5254228123947304 chr2 243199373 13563469 0.0557709867122067 0.3855275013215908 chr3 198022430 9990453 0.050451118087986295 0.25522162616809446 chr4 191154276 7059785 0.03693239381158285 0.22482899963508252 chr5 180915260 7513304 0.041529409956904684 0.2274772604628499 chr6 171115067 7290726 0.04260715393344059 0.26374340820285486 chr7 159138663 7633641 0.04796848770810648 0.43431185935468003 chr8 146364022 6924344 0.04730905795961251 0.30339176349016783 chr9 141213431 5217594 0.036948284331396214 0.2700362738181292 chr10 135534747 10067638 0.07428086319443973 0.46808068855824386 chr11 135006516 7745018 0.057367734754372894 0.3361126728199991 chr12 133851895 5610769 0.0419177404996769 0.2299442161772171 chr13 115169878 3636455 0.031574705670869944 0.19877514996298715 chr14 107349540 4401945 0.041005718329114406 0.23785704580191566 chr15 102531392 3403374 0.03319348283109236 0.21401926983407726 chr16 90354753 3355705 0.03713921944980581 0.2398051155607208 chr17 81195210 4239056 0.05220820292231525 0.2778560000457378 chr18 78077248 3551520 0.04548725897716067 0.4742276703197053 chr19 59128983 3342829 0.0565345255473107 0.39389649444990255 chr20 63025520 2840984 0.04507672447605351 0.24408397566186368 chr21 48129895 1461312 0.03036183644281792 0.20269068644862034 chr22 51304566 1242399 0.024216148714716737 0.1720718776179643 chrMT 16571 6354 0.3834409510590791 0.6964287272265421 chrX 155270560 9093495 0.058565480796874826 0.3050039102071685 chrY 59373566 327071 0.005508697254262949 0.11176728004321254