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Detailed information for vg1217862215:

Variant ID: vg1217862215 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 17862215
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.98, C: 0.03, others allele: 0.00, population size: 94. )

Flanking Sequence (100 bp) in Reference Genome:

CACTTAAGAAAGCATCTTCTGGAAAGTCCAAACCAGTCCCTCAGCTTGGAGCAACCAAACCAGGAGATCAAGCCGTTGGTGACCGGTGAAGAATTTGGAA[T/C]
ACAAGATTTTATTAATGACACCGGGCTAACTACGGATCAATTGCTACGAGGCGCACCAATCGAAAAGGCGGAAGTGAAATACATGTACGAACTCGGTAAA

Reverse complement sequence

TTTACCGAGTTCGTACATGTATTTCACTTCCGCCTTTTCGATTGGTGCGCCTCGTAGCAATTGATCCGTAGTTAGCCCGGTGTCATTAATAAAATCTTGT[A/G]
TTCCAAATTCTTCACCGGTCACCAACGGCTTGATCTCCTGGTTTGGTTGCTCCAAGCTGAGGGACTGGTTTGGACTTTCCAGAAGATGCTTTCTTAAGTG

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	59.30%	12.00%	0.99%	27.72%	NA
All Indica	2759	51.30%	19.20%	0.83%	28.63%	NA
All Japonica	1512	75.10%	0.50%	0.66%	23.74%	NA
Aus	269	52.40%	7.40%	4.09%	36.06%	NA
Indica I	595	83.70%	9.10%	0.17%	7.06%	NA
Indica II	465	48.20%	10.10%	1.94%	39.78%	NA
Indica III	913	31.40%	27.40%	0.55%	40.64%	NA
Indica Intermediate	786	51.70%	22.90%	1.02%	24.43%	NA
Temperate Japonica	767	97.80%	0.10%	0.13%	1.96%	NA
Tropical Japonica	504	46.80%	0.60%	1.59%	50.99%	NA
Japonica Intermediate	241	62.20%	1.20%	0.41%	36.10%	NA
VI/Aromatic	96	46.90%	2.10%	2.08%	48.96%	NA
Intermediate	90	72.20%	7.80%	1.11%	18.89%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1217862215	T -> C	LOC_Os12g29874.1	upstream_gene_variant ; 1940.0bp to feature; MODIFIER	silent_mutation	Average:14.419; most accessible tissue: Zhenshan97 flag leaf, score: 37.1	N	N	N	N
vg1217862215	T -> C	LOC_Os12g29860.1	downstream_gene_variant ; 12.0bp to feature; MODIFIER	silent_mutation	Average:14.419; most accessible tissue: Zhenshan97 flag leaf, score: 37.1	N	N	N	N
vg1217862215	T -> C	LOC_Os12g29860-LOC_Os12g29874	intergenic_region ; MODIFIER	silent_mutation	Average:14.419; most accessible tissue: Zhenshan97 flag leaf, score: 37.1	N	N	N	N
vg1217862215	T -> DEL	N	N	silent_mutation	Average:14.419; most accessible tissue: Zhenshan97 flag leaf, score: 37.1	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1217862215	4.63E-06	NA	mr1979	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
vg1217862215	5.64E-06	5.64E-06	mr1979	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