Search for Variation information by Variation ID:

Please input a variation ID (e.g., vg0722097923 , STR0500036000 ).

Detailed information for vg0316454459:

Variant ID: vg0316454459 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 16454459
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TTATTAAAAAAATTTATTTAAGTAATTATTAATTCTTTTCCTATCATTTGATTCATTGCTAATTATATTTTTATGTAGGCATATAATTTTACATATTTCA[T/C]
AAAAATTTTTAATAAGACGAACGGTCAAATATGTGCTAAAAAGTCAACGGTGTCAAATAGTTTGAAATGGAGGGAGTATATAAAACTTGCTGTTATAGAT

Reverse complement sequence

ATCTATAACAGCAAGTTTTATATACTCCCTCCATTTCAAACTATTTGACACCGTTGACTTTTTAGCACATATTTGACCGTTCGTCTTATTAAAAATTTTT[A/G]
TGAAATATGTAAAATTATATGCCTACATAAAAATATAATTAGCAATGAATCAAATGATAGGAAAAGAATTAATAATTACTTAAATAAATTTTTTTAATAA

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 64.40% 23.40% 0.30% 11.91% NA
All Indica  2759 82.30% 14.70% 0.22% 2.83% NA
All Japonica  1512 41.60% 30.80% 0.40% 27.25% NA
Aus  269 2.20% 75.80% 0.00% 21.93% NA
Indica I  595 94.30% 5.70% 0.00% 0.00% NA
Indica II  465 95.90% 2.40% 0.00% 1.72% NA
Indica III  913 71.10% 26.60% 0.11% 2.19% NA
Indica Intermediate  786 78.10% 14.90% 0.64% 6.36% NA
Temperate Japonica  767 51.90% 4.80% 0.65% 42.63% NA
Tropical Japonica  504 27.80% 63.50% 0.00% 8.73% NA
Japonica Intermediate  241 37.80% 44.80% 0.41% 17.01% NA
VI/Aromatic  96 85.40% 10.40% 0.00% 4.17% NA
Intermediate  90 61.10% 25.60% 2.22% 11.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0316454459 T -> C LOC_Os03g28990.1 upstream_gene_variant ; 3059.0bp to feature; MODIFIER silent_mutation Average:70.317; most accessible tissue: Callus, score: 98.849 N N N N
vg0316454459 T -> C LOC_Os03g28990.2 upstream_gene_variant ; 3059.0bp to feature; MODIFIER silent_mutation Average:70.317; most accessible tissue: Callus, score: 98.849 N N N N
vg0316454459 T -> C LOC_Os03g28980.1 downstream_gene_variant ; 2491.0bp to feature; MODIFIER silent_mutation Average:70.317; most accessible tissue: Callus, score: 98.849 N N N N
vg0316454459 T -> C LOC_Os03g28980-LOC_Os03g28990 intergenic_region ; MODIFIER silent_mutation Average:70.317; most accessible tissue: Callus, score: 98.849 N N N N
vg0316454459 T -> DEL N N silent_mutation Average:70.317; most accessible tissue: Callus, score: 98.849 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0316454459 NA 6.35E-10 mr1345 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
vg0316454459 NA 1.29E-06 mr1382 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
vg0316454459 NA 2.32E-06 mr1401 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
vg0316454459 NA 2.23E-09 mr1427 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
vg0316454459 NA 2.15E-07 mr1634 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
vg0316454459 NA 2.68E-08 mr1727 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
vg0316454459 NA 9.46E-07 mr1756 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
vg0316454459 NA 9.13E-06 mr1777 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
vg0316454459 NA 3.82E-06 mr1546_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
vg0316454459 NA 1.80E-06 mr1693_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
vg0316454459 NA 3.60E-08 mr1808_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