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Detailed information for vg1213936261:

Variant ID: vg1213936261 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 13936261
Reference Allele: C	Alternative Allele: G
Primary Allele: C	Secondary Allele: G

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.95, G: 0.05, others allele: 0.00, population size: 109. )

Flanking Sequence (100 bp) in Reference Genome:

AGGTTTAGAACCAGGCAGAGGTGCAGCCCACCTCCTGCCGACTATATCATACGCGATGTGCAGTAAAAACCCTAAAAAAATTTTCCCTAACTACACCGAA[C/G]
AAAACTTCAAAGCACACACATCATGTGGTTTCAGATCCAGGATGCTTTACTCGACATTGGGCAAAATCAACTCAAAAACATATACCCAGTAAACTCCAAA

Reverse complement sequence

TTTGGAGTTTACTGGGTATATGTTTTTGAGTTGATTTTGCCCAATGTCGAGTAAAGCATCCTGGATCTGAAACCACATGATGTGTGTGCTTTGAAGTTTT[G/C]
TTCGGTGTAGTTAGGGAAAATTTTTTTAGGGTTTTTACTGCACATCGCGTATGATATAGTCGGCAGGAGGTGGGCTGCACCTCTGCCTGGTTCTAAACCT

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	53.30%	19.00%	27.66%	0.00%	NA
All Indica	2759	47.80%	26.80%	25.37%	0.00%	NA
All Japonica	1512	57.10%	8.30%	34.66%	0.00%	NA
Aus	269	82.50%	2.60%	14.87%	0.00%	NA
Indica I	595	29.10%	40.80%	30.08%	0.00%	NA
Indica II	465	70.80%	10.50%	18.71%	0.00%	NA
Indica III	913	46.90%	29.20%	23.88%	0.00%	NA
Indica Intermediate	786	49.50%	23.00%	27.48%	0.00%	NA
Temperate Japonica	767	84.20%	2.50%	13.30%	0.00%	NA
Tropical Japonica	504	24.60%	14.90%	60.52%	0.00%	NA
Japonica Intermediate	241	38.60%	12.90%	48.55%	0.00%	NA
VI/Aromatic	96	67.70%	13.50%	18.75%	0.00%	NA
Intermediate	90	57.80%	14.40%	27.78%	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
vg1213936261	C -> G	LOC_Os12g24410.1	upstream_gene_variant ; 3699.0bp to feature; MODIFIER	silent_mutation	Average:29.709; most accessible tissue: Minghui63 young leaf, score: 42.042	N	N	N	N
vg1213936261	C -> G	LOC_Os12g24430.1	upstream_gene_variant ; 2534.0bp to feature; MODIFIER	silent_mutation	Average:29.709; most accessible tissue: Minghui63 young leaf, score: 42.042	N	N	N	N
vg1213936261	C -> G	LOC_Os12g24420.1	downstream_gene_variant ; 280.0bp to feature; MODIFIER	silent_mutation	Average:29.709; most accessible tissue: Minghui63 young leaf, score: 42.042	N	N	N	N
vg1213936261	C -> G	LOC_Os12g24410-LOC_Os12g24420	intergenic_region ; MODIFIER	silent_mutation	Average:29.709; most accessible tissue: Minghui63 young leaf, score: 42.042	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1213936261	NA	4.41E-06	mr1364	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
vg1213936261	NA	3.48E-09	mr1401	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
vg1213936261	NA	2.51E-06	mr1443	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
vg1213936261	NA	1.09E-06	mr1602	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