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Detailed information for vg1214380715:

Variant ID: vg1214380715 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 14380715
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.85, A: 0.15, others allele: 0.00, population size: 96. )

Flanking Sequence (100 bp) in Reference Genome:


TTAATTATATTCACCGGAAAAGGATCATGATCAAGCTTCATCTTGGAGCCATCGGTGAACTTCAATCGTCCTTCATCTATGGCCGATTGAACCTGTCGTC[A/G]
AAACACATTGCAATCATTAGTGGAATGAGAATGAGAATCATGCCATTTACAATAAGCTCGACGTTTCAATTCTTCTTGAGATGGTATGATATGGCCTTTA

Reverse complement sequence

TAAAGGCCATATCATACCATCTCAAGAAGAATTGAAACGTCGAGCTTATTGTAAATGGCATGATTCTCATTCTCATTCCACTAATGATTGCAATGTGTTT[T/C]
GACGACAGGTTCAATCGGCCATAGATGAAGGACGATTGAAGTTCACCGATGGCTCCAAGATGAAGCTTGATCATGATCCTTTTCCGGTGAATATAATTAA

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 26.80% 12.60% 1.71% 58.89% NA
All Indica  2759 16.80% 19.80% 2.61% 60.82% NA
All Japonica  1512 49.90% 2.80% 0.26% 46.96% NA
Aus  269 5.20% 0.40% 1.12% 93.31% NA
Indica I  595 22.20% 1.80% 1.68% 74.29% NA
Indica II  465 13.80% 35.30% 3.87% 47.10% NA
Indica III  913 16.50% 22.90% 2.85% 57.72% NA
Indica Intermediate  786 14.80% 20.60% 2.29% 62.34% NA
Temperate Japonica  767 79.00% 5.10% 0.13% 15.78% NA
Tropical Japonica  504 13.30% 0.00% 0.60% 86.11% NA
Japonica Intermediate  241 34.00% 1.70% 0.00% 64.32% NA
VI/Aromatic  96 4.20% 1.00% 1.04% 93.75% NA
Intermediate  90 35.60% 3.30% 1.11% 60.00% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1214380715 A -> DEL N N silent_mutation Average:6.922; most accessible tissue: Callus, score: 22.25 N N N N
vg1214380715 A -> G LOC_Os12g25050.1 intron_variant ; MODIFIER silent_mutation Average:6.922; most accessible tissue: Callus, score: 22.25 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1214380715 9.48E-06 NA mr1326 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