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Detailed information for vg1207363214:

Variant ID: vg1207363214 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 7363214
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.96, T: 0.03, others allele: 0.00, population size: 186. )

Flanking Sequence (100 bp) in Reference Genome:

TGCCGTATGTGTTTATCTCCTGCCATTCTCCTGATATCTCTCCCGACCTTCTTTTCTATAAGTCGGTTGAGTAGATAAGGGAAGGACGTGCCTATATGTA[C/T]
TCCTGCATATTGAGATCAATCCATTGCGTTGAGTCTATCTTGCTCTTATGCTGGACTATGGCTCGGTCATTTGCTTGCTACTTTGGAATTGGCTAGTTAG

Reverse complement sequence

CTAACTAGCCAATTCCAAAGTAGCAAGCAAATGACCGAGCCATAGTCCAGCATAAGAGCAAGATAGACTCAACGCAATGGATTGATCTCAATATGCAGGA[G/A]
TACATATAGGCACGTCCTTCCCTTATCTACTCAACCGACTTATAGAAAAGAAGGTCGGGAGAGATATCAGGAGAATGGCAGGAGATAAACACATACGGCA

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	41.20%	33.20%	3.17%	22.39%	NA
All Indica	2759	10.50%	54.50%	5.18%	29.87%	NA
All Japonica	1512	96.80%	2.70%	0.07%	0.46%	NA
Aus	269	33.10%	2.20%	0.74%	63.94%	NA
Indica I	595	3.00%	67.90%	4.87%	24.20%	NA
Indica II	465	14.40%	41.70%	7.31%	36.56%	NA
Indica III	913	11.80%	62.70%	2.85%	22.67%	NA
Indica Intermediate	786	12.20%	42.40%	6.87%	38.55%	NA
Temperate Japonica	767	98.80%	0.40%	0.13%	0.65%	NA
Tropical Japonica	504	93.70%	6.30%	0.00%	0.00%	NA
Japonica Intermediate	241	96.70%	2.50%	0.00%	0.83%	NA
VI/Aromatic	96	45.80%	0.00%	2.08%	52.08%	NA
Intermediate	90	70.00%	22.20%	2.22%	5.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1207363214	C -> DEL	N	N	silent_mutation	Average:64.925; most accessible tissue: Minghui63 flag leaf, score: 76.453	N	N	N	N
vg1207363214	C -> T	LOC_Os12g13209.1	upstream_gene_variant ; 3665.0bp to feature; MODIFIER	silent_mutation	Average:64.925; most accessible tissue: Minghui63 flag leaf, score: 76.453	N	N	N	N
vg1207363214	C -> T	LOC_Os12g13220.1	upstream_gene_variant ; 217.0bp to feature; MODIFIER	silent_mutation	Average:64.925; most accessible tissue: Minghui63 flag leaf, score: 76.453	N	N	N	N
vg1207363214	C -> T	LOC_Os12g13230.1	downstream_gene_variant ; 1584.0bp to feature; MODIFIER	silent_mutation	Average:64.925; most accessible tissue: Minghui63 flag leaf, score: 76.453	N	N	N	N
vg1207363214	C -> T	LOC_Os12g13209-LOC_Os12g13220	intergenic_region ; MODIFIER	silent_mutation	Average:64.925; most accessible tissue: Minghui63 flag leaf, score: 76.453	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1207363214	NA	3.14E-08	mr1804	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
vg1207363214	2.94E-07	8.38E-07	mr1912	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