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Detailed information for vg1208194851:

Variant ID: vg1208194851 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 8194851
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.90, C: 0.09, others allele: 0.00, population size: 68. )

Flanking Sequence (100 bp) in Reference Genome:

TAGGTGATTTATAATTTTCATTTAGGCTTGGGAAAGAAACTTCAGGGTGTGACACGAACCCCATGTAATCAGTTAACACACTCGTTCAATACAATTTCGG[T/C]
GCATCACCACCCTTTTGCTTTTGTTTTATTTCGACGAGTCCTTGCTTTCGGGTTGAGCTGCATCGGTTTCGATCTTCAACAAGAGGTAAAACTTGTTATG

Reverse complement sequence

CATAACAAGTTTTACCTCTTGTTGAAGATCGAAACCGATGCAGCTCAACCCGAAAGCAAGGACTCGTCGAAATAAAACAAAAGCAAAAGGGTGGTGATGC[A/G]
CCGAAATTGTATTGAACGAGTGTGTTAACTGATTACATGGGGTTCGTGTCACACCCTGAAGTTTCTTTCCCAAGCCTAAATGAAAATTATAAATCACCTA

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	49.50%	15.30%	9.06%	26.09%	NA
All Indica	2759	51.90%	22.10%	12.61%	13.37%	NA
All Japonica	1512	51.50%	2.20%	1.92%	44.38%	NA
Aus	269	19.70%	18.20%	11.90%	50.19%	NA
Indica I	595	43.20%	24.50%	16.97%	15.29%	NA
Indica II	465	43.70%	28.80%	17.63%	9.89%	NA
Indica III	913	60.70%	17.90%	8.00%	13.47%	NA
Indica Intermediate	786	53.20%	21.20%	11.70%	13.87%	NA
Temperate Japonica	767	74.40%	3.00%	2.61%	19.95%	NA
Tropical Japonica	504	23.40%	1.40%	0.79%	74.40%	NA
Japonica Intermediate	241	37.30%	1.20%	2.07%	59.34%	NA
VI/Aromatic	96	24.00%	20.80%	14.58%	40.62%	NA
Intermediate	90	58.90%	14.40%	5.56%	21.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1208194851	T -> C	LOC_Os12g14374.1	intron_variant ; MODIFIER	silent_mutation	Average:30.455; most accessible tissue: Zhenshan97 flag leaf, score: 47.303	N	N	N	N
vg1208194851	T -> DEL	N	N	silent_mutation	Average:30.455; most accessible tissue: Zhenshan97 flag leaf, score: 47.303	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1208194851	1.37E-06	NA	mr1178	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
vg1208194851	NA	1.01E-08	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
vg1208194851	NA	2.58E-06	mr1558	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
vg1208194851	NA	1.75E-07	mr1864_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