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Detailed information for vg0706567686:

Variant ID: vg0706567686 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 6567686
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


AGCTGAGAGTAAATCTTGTTTAGTGAAGAAAATAGTTAAGATTAAGATGAAAATCGTACCGAGTTTTGTAAACATAGTGTTTTTATTTTTGAAAGTATTA[T/C]
TAAATGGGAATTTCTCCCTTGGCCAACTTAGAAAAGGGGTGGGGCGCCTTTTTGGTCTTTTCCTACAGTCGTATGGCTCTGATACCAGCTTTGTGGACCC

Reverse complement sequence

GGGTCCACAAAGCTGGTATCAGAGCCATACGACTGTAGGAAAAGACCAAAAAGGCGCCCCACCCCTTTTCTAAGTTGGCCAAGGGAGAAATTCCCATTTA[A/G]
TAATACTTTCAAAAATAAAAACACTATGTTTACAAAACTCGGTACGATTTTCATCTTAATCTTAACTATTTTCTTCACTAAACAAGATTTACTCTCAGCT

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 72.60% 2.20% 3.45% 21.75% NA
All Indica  2759 59.00% 3.40% 5.15% 32.44% NA
All Japonica  1512 98.70% 0.00% 0.07% 1.26% NA
Aus  269 53.90% 3.70% 7.06% 35.32% NA
Indica I  595 65.50% 2.20% 4.54% 27.73% NA
Indica II  465 62.40% 1.70% 3.23% 32.69% NA
Indica III  913 52.40% 3.70% 7.67% 36.25% NA
Indica Intermediate  786 59.80% 5.00% 3.82% 31.42% NA
Temperate Japonica  767 98.20% 0.00% 0.00% 1.83% NA
Tropical Japonica  504 99.40% 0.00% 0.00% 0.60% NA
Japonica Intermediate  241 98.80% 0.00% 0.41% 0.83% NA
VI/Aromatic  96 97.90% 1.00% 0.00% 1.04% NA
Intermediate  90 78.90% 0.00% 1.11% 20.00% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0706567686 T -> DEL N N silent_mutation Average:13.799; most accessible tissue: Callus, score: 27.088 N N N N
vg0706567686 T -> C LOC_Os07g11860.1 upstream_gene_variant ; 360.0bp to feature; MODIFIER silent_mutation Average:13.799; most accessible tissue: Callus, score: 27.088 N N N N
vg0706567686 T -> C LOC_Os07g11860-LOC_Os07g11870 intergenic_region ; MODIFIER silent_mutation Average:13.799; most accessible tissue: Callus, score: 27.088 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0706567686 NA 8.64E-27 mr1309 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0706567686 NA 2.27E-08 mr1488 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0706567686 NA 2.05E-18 mr1566 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0706567686 NA 2.15E-08 mr1776 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0706567686 NA 1.58E-06 mr1886 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0706567686 NA 1.29E-35 mr1181_2 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0706567686 NA 4.27E-29 mr1238_2 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0706567686 NA 4.76E-07 mr1408_2 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0706567686 NA 2.06E-25 mr1484_2 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0706567686 NA 9.01E-22 mr1551_2 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0706567686 NA 6.93E-23 mr1609_2 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0706567686 NA 1.49E-07 mr1783_2 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0706567686 NA 3.84E-33 mr1841_2 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0706567686 NA 1.02E-20 mr1900_2 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0706567686 NA 3.16E-19 mr1945_2 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0706567686 NA 1.30E-09 mr1947_2 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0706567686 1.32E-06 NA mr1986_2 All YES Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251