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Detailed information for vg0414476036:

Variant ID: vg0414476036 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 14476036
Reference Allele: A	Alternative Allele: G,C
Primary Allele: A	Secondary Allele: C

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.89, G: 0.09, others allele: 0.00, population size: 45. )

Flanking Sequence (100 bp) in Reference Genome:

AAGAATAGAAAAACACGGCATTCTAATAGTATTATAAGTGCAAAACAGAGTATTGTAAAATATAGGAAAAAAGTGTAAAACAAAGAATTGCAAAATATAA[A/G,C]
AAAAACACAGAAATAACCGTTTGATTGGACTGCAGAAAAACGTAGGAATCAGATGAGAGAGATAGACTAAAAGGGAAACTTCTACGAAGTTGGAGCTCTT

Reverse complement sequence

AAGAGCTCCAACTTCGTAGAAGTTTCCCTTTTAGTCTATCTCTCTCATCTGATTCCTACGTTTTTCTGCAGTCCAATCAAACGGTTATTTCTGTGTTTTT[T/C,G]
TTATATTTTGCAATTCTTTGTTTTACACTTTTTTCCTATATTTTACAATACTCTGTTTTGCACTTATAATACTATTAGAATGCCGTGTTTTTCTATTCTT

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	20.10%	2.20%	1.29%	74.65%	G: 1.78%
All Indica	2759	6.70%	3.70%	1.20%	86.12%	G: 2.25%
All Japonica	1512	48.20%	0.00%	0.20%	51.06%	G: 0.53%
Aus	269	1.50%	0.00%	0.74%	95.54%	G: 2.23%
Indica I	595	18.70%	0.20%	0.84%	79.16%	G: 1.18%
Indica II	465	4.50%	0.00%	1.29%	87.96%	G: 6.24%
Indica III	913	3.00%	10.20%	1.53%	84.88%	G: 0.44%
Indica Intermediate	786	3.30%	1.10%	1.02%	91.73%	G: 2.80%
Temperate Japonica	767	84.00%	0.00%	0.00%	16.04%	NA
Tropical Japonica	504	4.00%	0.00%	0.40%	94.25%	G: 1.39%
Japonica Intermediate	241	27.00%	0.00%	0.41%	72.20%	G: 0.41%
VI/Aromatic	96	7.30%	0.00%	23.96%	66.67%	G: 2.08%
Intermediate	90	26.70%	1.10%	0.00%	65.56%	G: 6.67%

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0414476036	A -> C	LOC_Os04g25080-LOC_Os04g25100	intergenic_region ; MODIFIER	silent_mutation	Average:10.259; most accessible tissue: Callus, score: 39.085	N	N	N	N
vg0414476036	A -> DEL	N	N	silent_mutation	Average:10.259; most accessible tissue: Callus, score: 39.085	N	N	N	N
vg0414476036	A -> G	LOC_Os04g25080-LOC_Os04g25100	intergenic_region ; MODIFIER	silent_mutation	Average:10.259; most accessible tissue: Callus, score: 39.085	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0414476036	NA	6.98E-06	mr1011	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
vg0414476036	NA	9.51E-07	mr1330	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
vg0414476036	7.08E-06	NA	mr1549	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
vg0414476036	NA	9.20E-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
vg0414476036	NA	1.66E-12	mr1741	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
vg0414476036	NA	4.13E-08	mr1864	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
vg0414476036	NA	1.39E-07	mr1977	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
vg0414476036	NA	2.22E-06	mr1966_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