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Detailed information for vg0200790371:

Variant ID: vg0200790371 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 790371
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.92, T: 0.07, others allele: 0.00, population size: 291. )

Flanking Sequence (100 bp) in Reference Genome:


GAACAATTGAAAATGCTCAATTTTGTTATTCTGTGACAGCTTGAGCTTTGTTTTTTTTAACTTAAAAGACGTTGTTTTGTCTGAATTTCAAGGTAAAGTT[C/T]
AGCTACAAGTTAGAACTAGCTTGGTTTTGTATCATCCTGTTCATAGAGATTGTCAGGTGTGAGGATTACTTGTTGCCCAGCTTGGCCTGAAGATTGATGA

Reverse complement sequence

TCATCAATCTTCAGGCCAAGCTGGGCAACAAGTAATCCTCACACCTGACAATCTCTATGAACAGGATGATACAAAACCAAGCTAGTTCTAACTTGTAGCT[G/A]
AACTTTACCTTGAAATTCAGACAAAACAACGTCTTTTAAGTTAAAAAAAACAAAGCTCAAGCTGTCACAGAATAACAAAATTGAGCATTTTCAATTGTTC

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 79.30% 20.70% 0.06% 0.00% NA
All Indica  2759 94.70% 5.30% 0.00% 0.00% NA
All Japonica  1512 60.30% 39.60% 0.07% 0.00% NA
Aus  269 61.70% 37.90% 0.37% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 81.50% 18.50% 0.00% 0.00% NA
Indica III  913 98.50% 1.50% 0.00% 0.00% NA
Indica Intermediate  786 94.10% 5.90% 0.00% 0.00% NA
Temperate Japonica  767 83.20% 16.70% 0.13% 0.00% NA
Tropical Japonica  504 18.80% 81.20% 0.00% 0.00% NA
Japonica Intermediate  241 74.30% 25.70% 0.00% 0.00% NA
VI/Aromatic  96 2.10% 97.90% 0.00% 0.00% NA
Intermediate  90 60.00% 38.90% 1.11% 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
vg0200790371 C -> T LOC_Os02g02350.2 upstream_gene_variant ; 4695.0bp to feature; MODIFIER silent_mutation Average:61.479; most accessible tissue: Zhenshan97 root, score: 74.04 N N N N
vg0200790371 C -> T LOC_Os02g02360.1 downstream_gene_variant ; 1136.0bp to feature; MODIFIER silent_mutation Average:61.479; most accessible tissue: Zhenshan97 root, score: 74.04 N N N N
vg0200790371 C -> T LOC_Os02g02380.1 downstream_gene_variant ; 4695.0bp to feature; MODIFIER silent_mutation Average:61.479; most accessible tissue: Zhenshan97 root, score: 74.04 N N N N
vg0200790371 C -> T LOC_Os02g02370.1 intron_variant ; MODIFIER silent_mutation Average:61.479; most accessible tissue: Zhenshan97 root, score: 74.04 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0200790371 NA 2.96E-06 mr1029 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
vg0200790371 NA 3.95E-06 mr1092 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
vg0200790371 NA 1.16E-06 mr1154 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
vg0200790371 NA 1.84E-06 mr1189 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
vg0200790371 NA 5.62E-06 mr1415 Ind_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
vg0200790371 NA 3.93E-07 mr1502 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
vg0200790371 NA 5.62E-06 mr1567 Ind_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
vg0200790371 NA 1.56E-06 mr1625 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
vg0200790371 NA 4.93E-07 mr1642 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
vg0200790371 NA 1.01E-08 mr1680 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
vg0200790371 NA 2.38E-06 mr1684 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
vg0200790371 NA 6.28E-06 mr1742 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
vg0200790371 NA 8.55E-07 mr1796 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
vg0200790371 NA 1.23E-06 mr1990 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
vg0200790371 NA 9.25E-06 mr1559_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
vg0200790371 NA 6.19E-06 mr1928_2 Ind_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