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Detailed information for vg0630793825:

Variant ID: vg0630793825 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 30793825
Reference Allele: A	Alternative Allele: G
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, others allele: 0.00, population size: 254. )

Flanking Sequence (100 bp) in Reference Genome:

GACATCGCCGTGCTCAATCCTCAACGCGTTCACAATTTCCTCTTAAAAAAATATTTGGAGGGATGTCTCTCTCTTCAAATATCGTTTTTTTATGTCAACA[A/G]
GAGCAATTGATTTGTTAGGGAAAAAAGCAAGGTGCTAAGAATATCATCTTTTCTGTATTTTTTTTGGTATTCCCATGAATACCTAAGAATCCCGTTGGGT

Reverse complement sequence

ACCCAACGGGATTCTTAGGTATTCATGGGAATACCAAAAAAAATACAGAAAAGATGATATTCTTAGCACCTTGCTTTTTTCCCTAACAAATCAATTGCTC[T/C]
TGTTGACATAAAAAAACGATATTTGAAGAGAGAGACATCCCTCCAAATATTTTTTTAAGAGGAAATTGTGAACGCGTTGAGGATTGAGCACGGCGATGTC

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	77.50%	5.10%	2.60%	14.81%	NA
All Indica	2759	85.00%	0.10%	0.36%	14.57%	NA
All Japonica	1512	60.80%	15.70%	7.08%	16.34%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	99.00%	0.00%	0.34%	0.67%	NA
Indica II	465	80.60%	0.00%	0.22%	19.14%	NA
Indica III	913	77.00%	0.10%	0.55%	22.34%	NA
Indica Intermediate	786	86.30%	0.10%	0.25%	13.36%	NA
Temperate Japonica	767	56.80%	29.90%	12.78%	0.52%	NA
Tropical Japonica	504	54.40%	0.20%	0.60%	44.84%	NA
Japonica Intermediate	241	87.10%	3.30%	2.49%	7.05%	NA
VI/Aromatic	96	57.30%	0.00%	1.04%	41.67%	NA
Intermediate	90	80.00%	2.20%	5.56%	12.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0630793825	A -> G	LOC_Os06g50910.1	downstream_gene_variant ; 3287.0bp to feature; MODIFIER	silent_mutation	Average:49.673; most accessible tissue: Callus, score: 81.03	N	N	N	N
vg0630793825	A -> G	LOC_Os06g50890-LOC_Os06g50910	intergenic_region ; MODIFIER	silent_mutation	Average:49.673; most accessible tissue: Callus, score: 81.03	N	N	N	N
vg0630793825	A -> DEL	N	N	silent_mutation	Average:49.673; most accessible tissue: Callus, score: 81.03	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0630793825	2.34E-06	2.34E-06	mr1465	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