Search for Variation information by Variation ID:

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

Detailed information for vg1204019355:

Variant ID: vg1204019355 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 4019355
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.51, G: 0.49, others allele: 0.00, population size: 61. )

Flanking Sequence (100 bp) in Reference Genome:

TATGTTGAAGAACCAGAAATTGTTGATTTATGTGATGGGTCAGCTGATAACAGTAATTATGAGGCAGACATGGAATTAAAAGTGGACAGTGAAGAGGAGT[A/G]
TGTAAACATGGATGTTGAAGTTGATGTTGGTGAGGCTACTGGTAGTGGGTGCAAGGGTAAAGCGGTTGAAGAACATGGTGAGGCTAGTGGTAGTGGATCT

Reverse complement sequence

AGATCCACTACCACTAGCCTCACCATGTTCTTCAACCGCTTTACCCTTGCACCCACTACCAGTAGCCTCACCAACATCAACTTCAACATCCATGTTTACA[T/C]
ACTCCTCTTCACTGTCCACTTTTAATTCCATGTCTGCCTCATAATTACTGTTATCAGCTGACCCATCACATAAATCAACAATTTCTGGTTCTTCAACATA

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	24.70%	9.50%	0.34%	65.45%	NA
All Indica	2759	3.30%	4.50%	0.36%	91.92%	NA
All Japonica	1512	62.40%	19.30%	0.26%	17.99%	NA
Aus	269	5.90%	5.20%	0.74%	88.10%	NA
Indica I	595	1.70%	0.50%	0.50%	97.31%	NA
Indica II	465	1.70%	16.10%	0.86%	81.29%	NA
Indica III	913	3.60%	1.00%	0.22%	95.18%	NA
Indica Intermediate	786	5.00%	4.60%	0.13%	90.33%	NA
Temperate Japonica	767	83.30%	11.90%	0.39%	4.43%	NA
Tropical Japonica	504	41.90%	26.60%	0.00%	31.55%	NA
Japonica Intermediate	241	39.00%	27.80%	0.41%	32.78%	NA
VI/Aromatic	96	77.10%	8.30%	0.00%	14.58%	NA
Intermediate	90	47.80%	14.40%	0.00%	37.78%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1204019355	A -> DEL	N	N	silent_mutation	Average:11.056; most accessible tissue: Callus, score: 63.127	N	N	N	N
vg1204019355	A -> G	LOC_Os12g07910.1	3_prime_UTR_variant ; 1670.0bp to feature; MODIFIER	silent_mutation	Average:11.056; most accessible tissue: Callus, score: 63.127	N	N	N	N
vg1204019355	A -> G	LOC_Os12g07920.1	upstream_gene_variant ; 849.0bp to feature; MODIFIER	silent_mutation	Average:11.056; most accessible tissue: Callus, score: 63.127	N	N	N	N
vg1204019355	A -> G	LOC_Os12g07930.1	downstream_gene_variant ; 3329.0bp to feature; MODIFIER	silent_mutation	Average:11.056; most accessible tissue: Callus, score: 63.127	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1204019355	NA	1.03E-06	mr1653	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
vg1204019355	NA	9.30E-06	mr1679_2	Ind_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