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Detailed information for vg0231867258:

Variant ID: vg0231867258 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 31867258
Reference Allele: G	Alternative Allele: T
Primary Allele: G	Secondary Allele: T

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 38. )

Flanking Sequence (100 bp) in Reference Genome:

ACTCTAATTAATAAGCGAATAAAATATCATTACAGATGATGGAGCGTGGGGCTCCTCACCGGGAGGCCGCGCAGGCCCCCCTTTGCCGGTTCGGCCGGGG[G/T]
CGCTAAGTGAGGTTCTTCGCCCTCGATCTGAGGAACGTCAGCGAGAGAAGAAATGCGCAAGACACGGGCGACGTAGACAGGTTCGGGCCGCTGAGAAGCG

Reverse complement sequence

CGCTTCTCAGCGGCCCGAACCTGTCTACGTCGCCCGTGTCTTGCGCATTTCTTCTCTCGCTGACGTTCCTCAGATCGAGGGCGAAGAACCTCACTTAGCG[C/A]
CCCCGGCCGAACCGGCAAAGGGGGGCCTGCGCGGCCTCCCGGTGAGGAGCCCCACGCTCCATCATCTGTAATGATATTTTATTCGCTTATTAATTAGAGT

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	34.30%	1.60%	2.56%	61.51%	NA
All Indica	2759	1.70%	0.10%	3.52%	94.71%	NA
All Japonica	1512	94.00%	4.80%	0.86%	0.33%	NA
Aus	269	3.30%	0.00%	2.23%	94.42%	NA
Indica I	595	0.80%	0.00%	0.34%	98.82%	NA
Indica II	465	2.20%	0.20%	3.23%	94.41%	NA
Indica III	913	1.60%	0.00%	3.50%	94.85%	NA
Indica Intermediate	786	2.20%	0.10%	6.11%	91.60%	NA
Temperate Japonica	767	90.10%	8.10%	1.56%	0.26%	NA
Tropical Japonica	504	99.40%	0.60%	0.00%	0.00%	NA
Japonica Intermediate	241	95.40%	2.90%	0.41%	1.24%	NA
VI/Aromatic	96	91.70%	0.00%	0.00%	8.33%	NA
Intermediate	90	63.30%	1.10%	5.56%	30.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0231867258	G -> T	LOC_Os02g52060.1	upstream_gene_variant ; 1374.0bp to feature; MODIFIER	silent_mutation	Average:17.213; most accessible tissue: Callus, score: 43.323	N	N	N	N
vg0231867258	G -> T	LOC_Os02g52070.1	upstream_gene_variant ; 1528.0bp to feature; MODIFIER	silent_mutation	Average:17.213; most accessible tissue: Callus, score: 43.323	N	N	N	N
vg0231867258	G -> T	LOC_Os02g52060-LOC_Os02g52070	intergenic_region ; MODIFIER	silent_mutation	Average:17.213; most accessible tissue: Callus, score: 43.323	N	N	N	N
vg0231867258	G -> DEL	N	N	silent_mutation	Average:17.213; most accessible tissue: Callus, score: 43.323	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0231867258	NA	8.12E-07	mr1359_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
vg0231867258	5.85E-06	1.58E-06	mr1428_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
vg0231867258	1.06E-08	8.28E-09	mr1712_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
vg0231867258	1.40E-09	2.34E-09	mr1946_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
vg0231867258	1.40E-09	2.34E-09	mr1948_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
vg0231867258	5.56E-06	4.31E-07	mr1977_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