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Detailed information for vg0629505680:

Variant ID: vg0629505680 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 29505680
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.93, G: 0.08, others allele: 0.00, population size: 204. )

Flanking Sequence (100 bp) in Reference Genome:

TTCCTGACTGAGCTTGCTGAATCACATCAAGACCCTTGCAGAAAGGGACAATACCCCTTTGCTGAATGGCTGAAGGCTTCTCGAAACCTATAAAACAAAA[A/G]
AAAAGGTCTGATGAATAACAGTTCAAATGGCAAACACACAAAAAAAAAGCACGAAAGATTATAAACCTACCATAGGCATAGATGCCTCTGAGAAGGTTCT

Reverse complement sequence

AGAACCTTCTCAGAGGCATCTATGCCTATGGTAGGTTTATAATCTTTCGTGCTTTTTTTTTGTGTGTTTGCCATTTGAACTGTTATTCATCAGACCTTTT[T/C]
TTTTGTTTTATAGGTTTCGAGAAGCCTTCAGCCATTCAGCAAAGGGGTATTGTCCCTTTCTGCAAGGGTCTTGATGTGATTCAGCAAGCTCAGTCAGGAA

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	74.70%	25.20%	0.08%	0.00%	NA
All Indica	2759	73.60%	26.20%	0.14%	0.00%	NA
All Japonica	1512	84.40%	15.60%	0.00%	0.00%	NA
Aus	269	56.10%	43.90%	0.00%	0.00%	NA
Indica I	595	51.80%	48.20%	0.00%	0.00%	NA
Indica II	465	70.30%	29.50%	0.22%	0.00%	NA
Indica III	913	86.20%	13.70%	0.11%	0.00%	NA
Indica Intermediate	786	77.60%	22.10%	0.25%	0.00%	NA
Temperate Japonica	767	96.50%	3.50%	0.00%	0.00%	NA
Tropical Japonica	504	75.60%	24.40%	0.00%	0.00%	NA
Japonica Intermediate	241	64.30%	35.70%	0.00%	0.00%	NA
VI/Aromatic	96	9.40%	90.60%	0.00%	0.00%	NA
Intermediate	90	71.10%	28.90%	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
vg0629505680	A -> G	LOC_Os06g48740.1	downstream_gene_variant ; 2845.0bp to feature; MODIFIER	silent_mutation	Average:67.49; most accessible tissue: Callus, score: 78.092	N	N	N	N
vg0629505680	A -> G	LOC_Os06g48760.1	downstream_gene_variant ; 3144.0bp to feature; MODIFIER	silent_mutation	Average:67.49; most accessible tissue: Callus, score: 78.092	N	N	N	N
vg0629505680	A -> G	LOC_Os06g48760.2	downstream_gene_variant ; 3144.0bp to feature; MODIFIER	silent_mutation	Average:67.49; most accessible tissue: Callus, score: 78.092	N	N	N	N
vg0629505680	A -> G	LOC_Os06g48750.1	intron_variant ; MODIFIER	silent_mutation	Average:67.49; most accessible tissue: Callus, score: 78.092	N	N	N	N
vg0629505680	A -> G	LOC_Os06g48750.2	intron_variant ; MODIFIER	silent_mutation	Average:67.49; most accessible tissue: Callus, score: 78.092	N	N	N	N
vg0629505680	A -> G	LOC_Os06g48750.3	intron_variant ; MODIFIER	silent_mutation	Average:67.49; most accessible tissue: Callus, score: 78.092	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0629505680	NA	3.23E-07	mr1242_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
vg0629505680	NA	2.19E-06	mr1283_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
vg0629505680	NA	9.58E-06	mr1447_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
vg0629505680	2.85E-06	1.63E-06	mr1551_2	Ind_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
vg0629505680	NA	6.26E-06	mr1771_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
vg0629505680	NA	6.44E-07	mr1870_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