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Detailed information for vg0119570175:

Variant ID: vg0119570175 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 19570175
Reference Allele: G	Alternative Allele: A,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: 281. )

Flanking Sequence (100 bp) in Reference Genome:

GCATTAGGCCTCATTTTGCTCTGTTCCGCCGAATTTTCTTCCTCAAGCCCCAACCAAACAAGAGCAAACCATGCGTAGTTGGAGGGGCTGGATTTCAACT[G/A,T]
AGAGGAACCTTGAGCCAAAAGTATTTTTCTATGCCCTTCAAGACCTCAAACAAAGGATGGCACGCCAACTGGTTCTATGTCCAAAATCCTGAGCCTGCTC

Reverse complement sequence

GAGCAGGCTCAGGATTTTGGACATAGAACCAGTTGGCGTGCCATCCTTTGTTTGAGGTCTTGAAGGGCATAGAAAAATACTTTTGGCTCAAGGTTCCTCT[C/T,A]
AGTTGAAATCCAGCCCCTCCAACTACGCATGGTTTGCTCTTGTTTGGTTGGGGCTTGAGGAAGAAAATTCGGCGGAACAGAGCAAAATGAGGCCTAATGC

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	97.90%	0.10%	0.74%	1.14%	A: 0.11%
All Indica	2759	97.70%	0.00%	0.94%	1.16%	A: 0.18%
All Japonica	1512	98.90%	0.40%	0.53%	0.13%	NA
Aus	269	92.90%	0.00%	0.37%	6.69%	NA
Indica I	595	97.80%	0.00%	1.34%	0.84%	NA
Indica II	465	96.80%	0.00%	1.51%	1.29%	A: 0.43%
Indica III	913	98.90%	0.00%	0.22%	0.88%	NA
Indica Intermediate	786	96.80%	0.00%	1.15%	1.65%	A: 0.38%
Temperate Japonica	767	98.70%	0.50%	0.78%	0.00%	NA
Tropical Japonica	504	99.40%	0.00%	0.20%	0.40%	NA
Japonica Intermediate	241	98.80%	0.80%	0.41%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	97.80%	0.00%	0.00%	2.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0119570175	G -> T	LOC_Os01g35370.1	upstream_gene_variant ; 1064.0bp to feature; MODIFIER	silent_mutation	Average:48.747; most accessible tissue: Zhenshan97 flag leaf, score: 66.824	N	N	N	N
vg0119570175	G -> T	LOC_Os01g35380.1	upstream_gene_variant ; 31.0bp to feature; MODIFIER	silent_mutation	Average:48.747; most accessible tissue: Zhenshan97 flag leaf, score: 66.824	N	N	N	N
vg0119570175	G -> T	LOC_Os01g35390.1	downstream_gene_variant ; 2813.0bp to feature; MODIFIER	silent_mutation	Average:48.747; most accessible tissue: Zhenshan97 flag leaf, score: 66.824	N	N	N	N
vg0119570175	G -> T	LOC_Os01g35370-LOC_Os01g35380	intergenic_region ; MODIFIER	silent_mutation	Average:48.747; most accessible tissue: Zhenshan97 flag leaf, score: 66.824	N	N	N	N
vg0119570175	G -> A	LOC_Os01g35370.1	upstream_gene_variant ; 1064.0bp to feature; MODIFIER	silent_mutation	Average:48.747; most accessible tissue: Zhenshan97 flag leaf, score: 66.824	N	N	N	N
vg0119570175	G -> A	LOC_Os01g35380.1	upstream_gene_variant ; 31.0bp to feature; MODIFIER	silent_mutation	Average:48.747; most accessible tissue: Zhenshan97 flag leaf, score: 66.824	N	N	N	N
vg0119570175	G -> A	LOC_Os01g35390.1	downstream_gene_variant ; 2813.0bp to feature; MODIFIER	silent_mutation	Average:48.747; most accessible tissue: Zhenshan97 flag leaf, score: 66.824	N	N	N	N
vg0119570175	G -> A	LOC_Os01g35370-LOC_Os01g35380	intergenic_region ; MODIFIER	silent_mutation	Average:48.747; most accessible tissue: Zhenshan97 flag leaf, score: 66.824	N	N	N	N
vg0119570175	G -> DEL	N	N	silent_mutation	Average:48.747; most accessible tissue: Zhenshan97 flag leaf, score: 66.824	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0119570175	NA	1.75E-07	mr1310	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
vg0119570175	2.37E-06	2.37E-06	mr1926	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
vg0119570175	6.78E-06	9.42E-10	mr1310_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