Search for Variation information by Variation ID:

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

Detailed information for vg0315011517:

Variant ID: vg0315011517 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 15011517
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GATATGTCCAGGTATATATAGCTGCTACTAGATACTCCCTCTATTTTTTAATAGACGACGCCGTTGACTTTTTCTTCCATATTTGACTATTCGTCTTATT[C/T]
AAAAAATTTTATGTAAATATATAAAATATAAATCACACTTAAAGTATTATGAGTAATAAAACAACTCATAACAAAATAAATTACAATTACGTAAATTTTT

Reverse complement sequence

AAAAATTTACGTAATTGTAATTTATTTTGTTATGAGTTGTTTTATTACTCATAATACTTTAAGTGTGATTTATATTTTATATATTTACATAAAATTTTTT[G/A]
AATAAGACGAATAGTCAAATATGGAAGAAAAAGTCAACGGCGTCGTCTATTAAAAAATAGAGGGAGTATCTAGTAGCAGCTATATATACCTGGACATATC

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 79.10% 20.90% 0.00% 0.00% NA
All Indica  2759 99.50% 0.50% 0.00% 0.00% NA
All Japonica  1512 40.30% 59.70% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 99.80% 0.20% 0.00% 0.00% NA
Indica II  465 99.80% 0.20% 0.00% 0.00% NA
Indica III  913 98.80% 1.20% 0.00% 0.00% NA
Indica Intermediate  786 100.00% 0.00% 0.00% 0.00% NA
Temperate Japonica  767 11.60% 88.40% 0.00% 0.00% NA
Tropical Japonica  504 74.60% 25.40% 0.00% 0.00% NA
Japonica Intermediate  241 60.20% 39.80% 0.00% 0.00% NA
VI/Aromatic  96 42.70% 57.30% 0.00% 0.00% NA
Intermediate  90 82.20% 17.80% 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
vg0315011517 C -> T LOC_Os03g26240.1 upstream_gene_variant ; 2064.0bp to feature; MODIFIER silent_mutation Average:58.735; most accessible tissue: Callus, score: 78.971 N N N N
vg0315011517 C -> T LOC_Os03g26260.1 upstream_gene_variant ; 4289.0bp to feature; MODIFIER silent_mutation Average:58.735; most accessible tissue: Callus, score: 78.971 N N N N
vg0315011517 C -> T LOC_Os03g26229.1 downstream_gene_variant ; 3257.0bp to feature; MODIFIER silent_mutation Average:58.735; most accessible tissue: Callus, score: 78.971 N N N N
vg0315011517 C -> T LOC_Os03g26250.1 intron_variant ; MODIFIER silent_mutation Average:58.735; most accessible tissue: Callus, score: 78.971 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0315011517 NA 4.89E-06 mr1448 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
vg0315011517 NA 1.01E-09 mr1549 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
vg0315011517 NA 5.79E-09 mr1575 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
vg0315011517 NA 1.80E-06 mr1627 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
vg0315011517 NA 3.26E-08 mr1757 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
vg0315011517 NA 6.48E-07 mr1952_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