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Detailed information for vg0202318103:

Variant ID: vg0202318103 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 2318103
Reference Allele: GAlternative Allele: A
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.95, A: 0.05, others allele: 0.00, population size: 108. )

Flanking Sequence (100 bp) in Reference Genome:


ATGGGCGTTGGGTTGGATGGGAATATGGAATGATTCCTGAGCATTTTGTACCACCTCTCCAGGCAAAATTCACAAGTGTTGCAATGTTCAAGCAAAATTC[G/A]
TGTTCTGTACTATCAAATATAAGTTCGACATCCACAACTCATGTTCTCAGATAGGTACAGAATTTAAAGCAACTTTAGGTAACTAGTGACTGATGAGGAG

Reverse complement sequence

CTCCTCATCAGTCACTAGTTACCTAAAGTTGCTTTAAATTCTGTACCTATCTGAGAACATGAGTTGTGGATGTCGAACTTATATTTGATAGTACAGAACA[C/T]
GAATTTTGCTTGAACATTGCAACACTTGTGAATTTTGCCTGGAGAGGTGGTACAAAATGCTCAGGAATCATTCCATATTCCCATCCAACCCAACGCCCAT

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 60.00% 23.20% 0.19% 16.65% NA
All Indica  2759 92.50% 4.20% 0.07% 3.19% NA
All Japonica  1512 1.40% 55.20% 0.40% 42.99% NA
Aus  269 83.60% 5.60% 0.00% 10.78% NA
Indica I  595 92.40% 1.20% 0.17% 6.22% NA
Indica II  465 97.20% 2.40% 0.00% 0.43% NA
Indica III  913 91.10% 5.30% 0.11% 3.50% NA
Indica Intermediate  786 91.30% 6.50% 0.00% 2.16% NA
Temperate Japonica  767 0.30% 89.00% 0.13% 10.56% NA
Tropical Japonica  504 3.00% 10.30% 0.79% 85.91% NA
Japonica Intermediate  241 1.70% 41.50% 0.41% 56.43% NA
VI/Aromatic  96 3.10% 95.80% 0.00% 1.04% NA
Intermediate  90 36.70% 41.10% 1.11% 21.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0202318103 G -> A LOC_Os02g04950.1 3_prime_UTR_variant ; 1657.0bp to feature; MODIFIER silent_mutation Average:33.869; most accessible tissue: Zhenshan97 flower, score: 54.935 N N N N
vg0202318103 G -> A LOC_Os02g04945.1 upstream_gene_variant ; 887.0bp to feature; MODIFIER silent_mutation Average:33.869; most accessible tissue: Zhenshan97 flower, score: 54.935 N N N N
vg0202318103 G -> DEL N N silent_mutation Average:33.869; most accessible tissue: Zhenshan97 flower, score: 54.935 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0202318103 NA 3.47E-10 mr1623 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
vg0202318103 NA 1.17E-09 mr1714 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
vg0202318103 1.48E-06 1.49E-06 mr1067_2 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
vg0202318103 NA 1.52E-07 mr1068_2 Jap_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
vg0202318103 NA 1.50E-06 mr1078_2 Jap_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
vg0202318103 NA 7.33E-06 mr1112_2 Jap_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
vg0202318103 NA 1.82E-06 mr1155_2 Jap_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
vg0202318103 NA 2.69E-06 mr1200_2 Jap_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
vg0202318103 NA 1.21E-06 mr1253_2 Jap_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
vg0202318103 NA 1.04E-07 mr1335_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
vg0202318103 NA 4.54E-06 mr1620_2 Jap_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