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Detailed information for vg1204323650:

Variant ID: vg1204323650 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 4323650
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.76, T: 0.24, others allele: 0.00, population size: 42. )

Flanking Sequence (100 bp) in Reference Genome:

CAGGAGCTGGTCAGGGTTGCTGCAAGTGCCAAAGTTTGCACAGAACATGGTGGATCTGCTCAAGTTGATCTGCAAGCAATAGTTCCCCATTCCGAAAGCT[T/C]
CACAACTGCATCTGTGAGGCTGACATCTGGCAAGGAAACTGTGTCTGTCTCAGCTGAAGAGCCTACAAAAAATCTGCCAAAGAAGAAAGCTGGAGGAGCT

Reverse complement sequence

AGCTCCTCCAGCTTTCTTCTTTGGCAGATTTTTTGTAGGCTCTTCAGCTGAGACAGACACAGTTTCCTTGCCAGATGTCAGCCTCACAGATGCAGTTGTG[A/G]
AGCTTTCGGAATGGGGAACTATTGCTTGCAGATCAACTTGAGCAGATCCACCATGTTCTGTGCAAACTTTGGCACTTGCAGCAACCCTGACCAGCTCCTG

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	24.60%	13.90%	6.09%	55.42%	NA
All Indica	2759	6.30%	20.70%	10.04%	62.89%	NA
All Japonica	1512	57.90%	0.20%	0.13%	41.73%	NA
Aus	269	24.20%	27.50%	0.00%	48.33%	NA
Indica I	595	8.10%	49.20%	28.91%	13.78%	NA
Indica II	465	8.40%	8.40%	1.51%	81.72%	NA
Indica III	913	1.20%	11.40%	4.27%	83.13%	NA
Indica Intermediate	786	9.80%	17.30%	7.51%	65.39%	NA
Temperate Japonica	767	84.10%	0.10%	0.26%	15.51%	NA
Tropical Japonica	504	28.60%	0.20%	0.00%	71.23%	NA
Japonica Intermediate	241	36.10%	0.40%	0.00%	63.49%	NA
VI/Aromatic	96	15.60%	2.10%	2.08%	80.21%	NA
Intermediate	90	34.40%	6.70%	7.78%	51.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1204323650	T -> C	LOC_Os12g08510.1	upstream_gene_variant ; 2902.0bp to feature; MODIFIER	silent_mutation	Average:12.433; most accessible tissue: Callus, score: 29.839	N	N	N	N
vg1204323650	T -> C	LOC_Os12g08530.1	downstream_gene_variant ; 812.0bp to feature; MODIFIER	silent_mutation	Average:12.433; most accessible tissue: Callus, score: 29.839	N	N	N	N
vg1204323650	T -> C	LOC_Os12g08510-LOC_Os12g08530	intergenic_region ; MODIFIER	silent_mutation	Average:12.433; most accessible tissue: Callus, score: 29.839	N	N	N	N
vg1204323650	T -> DEL	N	N	silent_mutation	Average:12.433; most accessible tissue: Callus, score: 29.839	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1204323650	NA	9.84E-06	mr1125	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
vg1204323650	2.25E-06	1.13E-07	mr1125_2	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