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Detailed information for vg0202124487:

Variant ID: vg0202124487 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 2124487
Reference Allele: C	Alternative Allele: G
Primary Allele: C	Secondary Allele: G

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.01, G: 0.00, others allele: 0.00, population size: 209. )

Flanking Sequence (100 bp) in Reference Genome:

CTAACAAACTCTAAGATACCATAAGTCTTTGCGGCAGATTTTTGGCCAAACATATCTCTAAGGAAGTTACATAAAACATCCTAATTAATAAATACAATTG[C/G]
CTTCTCAGGACTCTATCCATGTGCGGCAATCATCTTGAAGCACCTCAATTCAACCCAATGTCATACACCAAATTATACTGTCAGAATCGGCTGCATCGGC

Reverse complement sequence

GCCGATGCAGCCGATTCTGACAGTATAATTTGGTGTATGACATTGGGTTGAATTGAGGTGCTTCAAGATGATTGCCGCACATGGATAGAGTCCTGAGAAG[G/C]
CAATTGTATTTATTAATTAGGATGTTTTATGTAACTTCCTTAGAGATATGTTTGGCCAAAAATCTGCCGCAAAGACTTATGGTATCTTAGAGTTTGTTAG

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	63.50%	36.50%	0.02%	0.00%	NA
All Indica	2759	45.70%	54.20%	0.04%	0.00%	NA
All Japonica	1512	99.50%	0.50%	0.00%	0.00%	NA
Aus	269	24.90%	75.10%	0.00%	0.00%	NA
Indica I	595	47.10%	52.90%	0.00%	0.00%	NA
Indica II	465	34.40%	65.40%	0.22%	0.00%	NA
Indica III	913	55.90%	44.10%	0.00%	0.00%	NA
Indica Intermediate	786	39.70%	60.30%	0.00%	0.00%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	98.80%	1.20%	0.00%	0.00%	NA
Japonica Intermediate	241	99.20%	0.80%	0.00%	0.00%	NA
VI/Aromatic	96	97.90%	2.10%	0.00%	0.00%	NA
Intermediate	90	81.10%	18.90%	0.00%	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
vg0202124487	C -> G	LOC_Os02g04690.1	upstream_gene_variant ; 4068.0bp to feature; MODIFIER	silent_mutation	Average:61.814; most accessible tissue: Minghui63 root, score: 80.76	N	N	N	N
vg0202124487	C -> G	LOC_Os02g04700.1	upstream_gene_variant ; 796.0bp to feature; MODIFIER	silent_mutation	Average:61.814; most accessible tissue: Minghui63 root, score: 80.76	N	N	N	N
vg0202124487	C -> G	LOC_Os02g04690.2	upstream_gene_variant ; 4068.0bp to feature; MODIFIER	silent_mutation	Average:61.814; most accessible tissue: Minghui63 root, score: 80.76	N	N	N	N
vg0202124487	C -> G	LOC_Os02g04700.2	upstream_gene_variant ; 409.0bp to feature; MODIFIER	silent_mutation	Average:61.814; most accessible tissue: Minghui63 root, score: 80.76	N	N	N	N
vg0202124487	C -> G	LOC_Os02g04710.1	downstream_gene_variant ; 3742.0bp to feature; MODIFIER	silent_mutation	Average:61.814; most accessible tissue: Minghui63 root, score: 80.76	N	N	N	N
vg0202124487	C -> G	LOC_Os02g04710.2	downstream_gene_variant ; 3742.0bp to feature; MODIFIER	silent_mutation	Average:61.814; most accessible tissue: Minghui63 root, score: 80.76	N	N	N	N
vg0202124487	C -> G	LOC_Os02g04690-LOC_Os02g04700	intergenic_region ; MODIFIER	silent_mutation	Average:61.814; most accessible tissue: Minghui63 root, score: 80.76	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0202124487	2.50E-06	NA	mr1350_2	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
vg0202124487	6.87E-06	5.75E-06	mr1350_2	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