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Detailed information for vg0226545270:

Variant ID: vg0226545270 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 26545270
Reference Allele: C	Alternative Allele: G
Primary Allele: C	Secondary Allele: G

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 259. )

Flanking Sequence (100 bp) in Reference Genome:

TCACTTTATATCTTCAGTTTTTCACAGTATTTTTTATAAGAGTTTACTGGGAATTCGATTTTAAACCTAGGGCTCAAGTCCTAACTCCTAACTGCTCCAC[C/G]
CTTGTCTTCCGCGTGAATTTGATTCCAATGAAACTATAGAATTTTCGTTCAATTAATTTTGGGTATTCTAGGGAGATTAAGCAAAGTGCCCACAACAATC

Reverse complement sequence

GATTGTTGTGGGCACTTTGCTTAATCTCCCTAGAATACCCAAAATTAATTGAACGAAAATTCTATAGTTTCATTGGAATCAAATTCACGCGGAAGACAAG[G/C]
GTGGAGCAGTTAGGAGTTAGGACTTGAGCCCTAGGTTTAAAATCGAATTCCCAGTAAACTCTTATAAAAAATACTGTGAAAAACTGAAGATATAAAGTGA

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	89.40%	10.30%	0.30%	0.00%	NA
All Indica	2759	96.00%	3.90%	0.04%	0.00%	NA
All Japonica	1512	75.40%	23.90%	0.66%	0.00%	NA
Aus	269	98.50%	1.50%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	100.00%	0.00%	0.00%	0.00%	NA
Indica III	913	88.70%	11.20%	0.11%	0.00%	NA
Indica Intermediate	786	99.20%	0.80%	0.00%	0.00%	NA
Temperate Japonica	767	88.80%	10.20%	1.04%	0.00%	NA
Tropical Japonica	504	62.50%	37.30%	0.20%	0.00%	NA
Japonica Intermediate	241	59.80%	39.80%	0.41%	0.00%	NA
VI/Aromatic	96	97.90%	1.00%	1.04%	0.00%	NA
Intermediate	90	84.40%	13.30%	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
vg0226545270	C -> G	LOC_Os02g43950.1	downstream_gene_variant ; 311.0bp to feature; MODIFIER	silent_mutation	Average:50.756; most accessible tissue: Callus, score: 76.585	N	N	N	N
vg0226545270	C -> G	LOC_Os02g43960.1	downstream_gene_variant ; 1202.0bp to feature; MODIFIER	silent_mutation	Average:50.756; most accessible tissue: Callus, score: 76.585	N	N	N	N
vg0226545270	C -> G	LOC_Os02g43950-LOC_Os02g43960	intergenic_region ; MODIFIER	silent_mutation	Average:50.756; most accessible tissue: Callus, score: 76.585	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0226545270	1.77E-06	NA	mr1117	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
vg0226545270	NA	1.48E-07	mr1117	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
vg0226545270	NA	6.81E-06	mr1120	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
vg0226545270	6.12E-07	NA	mr1240	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
vg0226545270	NA	2.04E-06	mr1240	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
vg0226545270	6.72E-06	NA	mr1247	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
vg0226545270	NA	8.87E-07	mr1247	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
vg0226545270	NA	2.56E-08	mr1691	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
vg0226545270	1.24E-06	NA	mr1113_2	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
vg0226545270	NA	8.84E-07	mr1113_2	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
vg0226545270	9.15E-07	NA	mr1117_2	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
vg0226545270	NA	4.05E-07	mr1117_2	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
vg0226545270	NA	7.35E-07	mr1119_2	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
vg0226545270	NA	2.55E-06	mr1120_2	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
vg0226545270	NA	2.63E-06	mr1240_2	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
vg0226545270	NA	5.99E-06	mr1247_2	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
vg0226545270	NA	1.06E-09	mr1851_2	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
vg0226545270	NA	2.44E-06	mr1966_2	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