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Detailed information for vg0703429473:

Variant ID: vg0703429473 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 3429473
Reference Allele: AAlternative Allele: C
Primary Allele: ASecondary Allele: C

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.80, C: 0.20, others allele: 0.00, population size: 209. )

Flanking Sequence (100 bp) in Reference Genome:


ATCTTAAAAAATAAATTAATATAATCTCTTAAAGCAACTTTCCTATAATTTTTTTTAAAAAAACACATTATTTAGCTATTCGGAAAATACGCACGTGGAA[A/C]
ACAAGATTGGTGAAATTGGCAACATTGACTTTAGAACACAGCCCAAGGCATTAACCCACCAACATCCGGGGACACGATCTTGAGTTGAGTTTCCTACTGA

Reverse complement sequence

TCAGTAGGAAACTCAACTCAAGATCGTGTCCCCGGATGTTGGTGGGTTAATGCCTTGGGCTGTGTTCTAAAGTCAATGTTGCCAATTTCACCAATCTTGT[T/G]
TTCCACGTGCGTATTTTCCGAATAGCTAAATAATGTGTTTTTTTAAAAAAAATTATAGGAAAGTTGCTTTAAGAGATTATATTAATTTATTTTTTAAGAT

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 56.00% 43.60% 0.34% 0.02% NA
All Indica  2759 35.90% 63.60% 0.47% 0.04% NA
All Japonica  1512 99.70% 0.30% 0.00% 0.00% NA
Aus  269 3.30% 96.70% 0.00% 0.00% NA
Indica I  595 84.70% 15.00% 0.17% 0.17% NA
Indica II  465 15.10% 84.10% 0.86% 0.00% NA
Indica III  913 16.00% 83.70% 0.33% 0.00% NA
Indica Intermediate  786 34.40% 65.00% 0.64% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 99.20% 0.80% 0.00% 0.00% NA
Japonica Intermediate  241 99.60% 0.40% 0.00% 0.00% NA
VI/Aromatic  96 90.60% 9.40% 0.00% 0.00% NA
Intermediate  90 60.00% 36.70% 3.33% 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
vg0703429473 A -> DEL N N silent_mutation Average:67.671; most accessible tissue: Callus, score: 93.643 N N N N
vg0703429473 A -> C LOC_Os07g06970.1 3_prime_UTR_variant ; 202.0bp to feature; MODIFIER silent_mutation Average:67.671; most accessible tissue: Callus, score: 93.643 N N N N
vg0703429473 A -> C LOC_Os07g06960.1 upstream_gene_variant ; 1006.0bp to feature; MODIFIER silent_mutation Average:67.671; most accessible tissue: Callus, score: 93.643 N N N N
vg0703429473 A -> C LOC_Os07g06950.1 downstream_gene_variant ; 4966.0bp to feature; MODIFIER silent_mutation Average:67.671; most accessible tissue: Callus, score: 93.643 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0703429473 NA 2.56E-07 mr1291 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
vg0703429473 NA 9.57E-06 mr1531 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
vg0703429473 NA 2.19E-17 mr1557 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
vg0703429473 NA 9.18E-06 mr1679 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
vg0703429473 NA 6.89E-06 mr1904 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
vg0703429473 NA 1.21E-07 mr1659_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
vg0703429473 NA 6.18E-06 mr1974_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