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Detailed information for vg1222656354:

Variant ID: vg1222656354 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 22656354
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, T: 0.00, others allele: 0.00, population size: 268. )

Flanking Sequence (100 bp) in Reference Genome:

AAGTTATATTTCCAAAATGTTATAATTCTCTCTCTCTCTCTCTCTCTCGTAAGGATGGAGTACTTTATAAATCAAGACGCAAGAACGTGAATATCACTAG[C/T]
AGTGTTAACACAACGATTTCACAGAAGAATAAACAGGTAAGATAATGCAAGTTTTCATTTTAACTTGAACGGAGCACGGGTTTAACAGGATACAATTACT

Reverse complement sequence

AGTAATTGTATCCTGTTAAACCCGTGCTCCGTTCAAGTTAAAATGAAAACTTGCATTATCTTACCTGTTTATTCTTCTGTGAAATCGTTGTGTTAACACT[G/A]
CTAGTGATATTCACGTTCTTGCGTCTTGATTTATAAAGTACTCCATCCTTACGAGAGAGAGAGAGAGAGAGAGAATTATAACATTTTGGAAATATAACTT

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	88.60%	10.20%	1.18%	0.00%	NA
All Indica	2759	95.00%	4.30%	0.72%	0.00%	NA
All Japonica	1512	86.50%	11.60%	1.85%	0.00%	NA
Aus	269	36.10%	61.70%	2.23%	0.00%	NA
Indica I	595	89.20%	7.70%	3.03%	0.00%	NA
Indica II	465	97.80%	1.90%	0.22%	0.00%	NA
Indica III	913	96.70%	3.30%	0.00%	0.00%	NA
Indica Intermediate	786	95.50%	4.30%	0.13%	0.00%	NA
Temperate Japonica	767	94.90%	2.90%	2.22%	0.00%	NA
Tropical Japonica	504	73.00%	25.80%	1.19%	0.00%	NA
Japonica Intermediate	241	88.00%	10.00%	2.07%	0.00%	NA
VI/Aromatic	96	90.60%	9.40%	0.00%	0.00%	NA
Intermediate	90	83.30%	14.40%	2.22%	0.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1222656354	C -> T	LOC_Os12g36940.1	downstream_gene_variant ; 84.0bp to feature; MODIFIER	silent_mutation	Average:71.374; most accessible tissue: Zhenshan97 root, score: 80.909	N	N	N	N
vg1222656354	C -> T	LOC_Os12g36950.1	downstream_gene_variant ; 20.0bp to feature; MODIFIER	silent_mutation	Average:71.374; most accessible tissue: Zhenshan97 root, score: 80.909	N	N	N	N
vg1222656354	C -> T	LOC_Os12g36950.3	downstream_gene_variant ; 20.0bp to feature; MODIFIER	silent_mutation	Average:71.374; most accessible tissue: Zhenshan97 root, score: 80.909	N	N	N	N
vg1222656354	C -> T	LOC_Os12g36940-LOC_Os12g36950	intergenic_region ; MODIFIER	silent_mutation	Average:71.374; most accessible tissue: Zhenshan97 root, score: 80.909	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1222656354	6.30E-06	NA	mr1383	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
vg1222656354	4.59E-06	NA	mr1383	Jap_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
vg1222656354	NA	8.18E-06	mr1564	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
vg1222656354	NA	1.12E-06	mr1676	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
vg1222656354	8.73E-06	2.95E-06	mr1857	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