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Detailed information for vg1208780205:

Variant ID: vg1208780205 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 8780205
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.99, C: 0.02, others allele: 0.00, population size: 90. )

Flanking Sequence (100 bp) in Reference Genome:

TAACATGGCACCTTGCAATTTGATTACTGCGTTAACAAGAAAAATGATAGGTGGATAATTAAAGTAAGAGTGATTAGGATATGGGAAGCGGTTAATCCTA[T/C]
AATGGCTGATGAGTTCTATGGTATACGCGGATGATTCTACTAGATGCAGAGGTATGATTGTTGCAAACATATCATTTAATATATTGTTCTATTATGTAAA

Reverse complement sequence

TTTACATAATAGAACAATATATTAAATGATATGTTTGCAACAATCATACCTCTGCATCTAGTAGAATCATCCGCGTATACCATAGAACTCATCAGCCATT[A/G]
TAGGATTAACCGCTTCCCATATCCTAATCACTCTTACTTTAATTATCCACCTATCATTTTTCTTGTTAACGCAGTAATCAAATTGCAAGGTGCCATGTTA

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	72.00%	2.80%	18.05%	7.11%	NA
All Indica	2759	58.90%	0.90%	28.63%	11.56%	NA
All Japonica	1512	97.20%	0.10%	2.05%	0.66%	NA
Aus	269	70.30%	27.50%	1.86%	0.37%	NA
Indica I	595	57.60%	0.30%	27.06%	14.96%	NA
Indica II	465	51.40%	1.10%	31.83%	15.70%	NA
Indica III	913	63.40%	1.00%	27.82%	7.78%	NA
Indica Intermediate	786	58.90%	1.30%	28.88%	10.94%	NA
Temperate Japonica	767	96.20%	0.10%	2.74%	0.91%	NA
Tropical Japonica	504	97.80%	0.00%	1.79%	0.40%	NA
Japonica Intermediate	241	99.20%	0.00%	0.41%	0.41%	NA
VI/Aromatic	96	53.10%	25.00%	17.71%	4.17%	NA
Intermediate	90	76.70%	10.00%	11.11%	2.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1208780205	T -> C	LOC_Os12g15370-LOC_Os12g15390	intergenic_region ; MODIFIER	silent_mutation	Average:21.754; most accessible tissue: Callus, score: 44.136	N	N	N	N
vg1208780205	T -> DEL	N	N	silent_mutation	Average:21.754; most accessible tissue: Callus, score: 44.136	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1208780205	NA	4.74E-09	mr1425	Ind_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
vg1208780205	NA	9.13E-08	mr1002_2	Ind_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
vg1208780205	NA	1.11E-06	mr1015_2	Ind_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
vg1208780205	7.49E-07	1.58E-11	mr1864_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