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Detailed information for vg0603069706:

Variant ID: vg0603069706 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 3069706
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.77, T: 0.23, others allele: 0.00, population size: 81. )

Flanking Sequence (100 bp) in Reference Genome:

ATATTACGGACGCAACAATCGTTTTAATATATCAGCAGGCTTATACTTGAAAAAAATCAGCAATTGCAAGCACATACGTAATTAAGCTCGTATTAATTGG[C/T]
TTGTAATTTACAAATTTTCCCTTGTTTTCCTCAAGTTTTGCCCTTTTTTGCTGTCATCGTAATTTACAAGTATTACGCCTTGCAAATGCACATGAACGAA

Reverse complement sequence

TTCGTTCATGTGCATTTGCAAGGCGTAATACTTGTAAATTACGATGACAGCAAAAAAGGGCAAAACTTGAGGAAAACAAGGGAAAATTTGTAAATTACAA[G/A]
CCAATTAATACGAGCTTAATTACGTATGTGCTTGCAATTGCTGATTTTTTTCAAGTATAAGCCTGCTGATATATTAAAACGATTGTTGCGTCCGTAATAT

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	40.90%	10.10%	0.11%	48.98%	NA
All Indica	2759	14.70%	15.10%	0.11%	70.10%	NA
All Japonica	1512	95.60%	3.60%	0.00%	0.73%	NA
Aus	269	1.90%	0.00%	0.74%	97.40%	NA
Indica I	595	3.90%	25.70%	0.17%	70.25%	NA
Indica II	465	50.30%	23.20%	0.22%	26.24%	NA
Indica III	913	3.20%	0.40%	0.00%	96.39%	NA
Indica Intermediate	786	15.30%	19.20%	0.13%	65.39%	NA
Temperate Japonica	767	99.60%	0.30%	0.00%	0.13%	NA
Tropical Japonica	504	97.40%	1.40%	0.00%	1.19%	NA
Japonica Intermediate	241	79.30%	19.10%	0.00%	1.66%	NA
VI/Aromatic	96	16.70%	0.00%	0.00%	83.33%	NA
Intermediate	90	64.40%	4.40%	0.00%	31.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0603069706	C -> T	LOC_Os06g06540.1	downstream_gene_variant ; 969.0bp to feature; MODIFIER	silent_mutation	Average:20.198; most accessible tissue: Callus, score: 51.71	N	N	N	N
vg0603069706	C -> T	LOC_Os06g06550.1	downstream_gene_variant ; 4480.0bp to feature; MODIFIER	silent_mutation	Average:20.198; most accessible tissue: Callus, score: 51.71	N	N	N	N
vg0603069706	C -> T	LOC_Os06g06540-LOC_Os06g06550	intergenic_region ; MODIFIER	silent_mutation	Average:20.198; most accessible tissue: Callus, score: 51.71	N	N	N	N
vg0603069706	C -> DEL	N	N	silent_mutation	Average:20.198; most accessible tissue: Callus, score: 51.71	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0603069706	NA	6.97E-06	mr1005	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
vg0603069706	NA	9.46E-10	mr1011	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
vg0603069706	NA	2.38E-07	mr1011	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
vg0603069706	3.62E-06	3.61E-06	mr1012	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
vg0603069706	NA	1.62E-06	mr1706	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
vg0603069706	NA	8.33E-06	mr1439_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