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Detailed information for vg0317658313:

Variant ID: vg0317658313 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 17658313
Reference Allele: GAlternative Allele: A
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GCGTCCCAAATCAAGATGAAAATCAAAAGAGCCAAAAAAAAATATCGATTGTAATCCGGTGAAAATTATGTCGCCCAAACCCGAAAAGAGTTACTCCCAT[G/A]
TACTAGAAATATAAAAATACCGCTAATTGCACGTGTAATTTTATATAATACTCTCTCCATCCCTAAATATTTGACGCCGTTGACTTAAAAGAAATTGAAA

Reverse complement sequence

TTTCAATTTCTTTTAAGTCAACGGCGTCAAATATTTAGGGATGGAGAGAGTATTATATAAAATTACACGTGCAATTAGCGGTATTTTTATATTTCTAGTA[C/T]
ATGGGAGTAACTCTTTTCGGGTTTGGGCGACATAATTTTCACCGGATTACAATCGATATTTTTTTTTGGCTCTTTTGATTTTCATCTTGATTTGGGACGC

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 66.40% 33.60% 0.02% 0.00% NA
All Indica  2759 98.00% 2.00% 0.04% 0.00% NA
All Japonica  1512 8.00% 92.00% 0.00% 0.00% NA
Aus  269 91.40% 8.60% 0.00% 0.00% NA
Indica I  595 98.20% 1.70% 0.17% 0.00% NA
Indica II  465 97.40% 2.60% 0.00% 0.00% NA
Indica III  913 99.00% 1.00% 0.00% 0.00% NA
Indica Intermediate  786 96.90% 3.10% 0.00% 0.00% NA
Temperate Japonica  767 0.30% 99.70% 0.00% 0.00% NA
Tropical Japonica  504 21.20% 78.80% 0.00% 0.00% NA
Japonica Intermediate  241 5.00% 95.00% 0.00% 0.00% NA
VI/Aromatic  96 17.70% 82.30% 0.00% 0.00% NA
Intermediate  90 55.60% 44.40% 0.00% 0.00% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0317658313 G -> A LOC_Os03g30990.1 upstream_gene_variant ; 3800.0bp to feature; MODIFIER silent_mutation Average:51.288; most accessible tissue: Zhenshan97 flower, score: 70.434 N N N N
vg0317658313 G -> A LOC_Os03g31000.1 upstream_gene_variant ; 1699.0bp to feature; MODIFIER silent_mutation Average:51.288; most accessible tissue: Zhenshan97 flower, score: 70.434 N N N N
vg0317658313 G -> A LOC_Os03g30990-LOC_Os03g31000 intergenic_region ; MODIFIER silent_mutation Average:51.288; most accessible tissue: Zhenshan97 flower, score: 70.434 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0317658313 NA 4.70E-09 mr1198 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
vg0317658313 NA 7.20E-14 mr1218 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
vg0317658313 NA 6.51E-14 mr1376 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
vg0317658313 NA 6.51E-14 mr1431 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
vg0317658313 NA 1.09E-77 mr1718 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
vg0317658313 6.05E-09 4.31E-130 mr1750 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
vg0317658313 1.12E-08 1.68E-09 mr1860 Jap_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
vg0317658313 NA 1.90E-40 mr1873 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
vg0317658313 NA 8.10E-08 mr1645_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
vg0317658313 NA 8.34E-13 mr1713_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
vg0317658313 1.98E-06 6.22E-114 mr1718_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
vg0317658313 1.54E-08 8.83E-166 mr1750_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