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Detailed information for vg1001428076:

Variant ID: vg1001428076 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 1428076
Reference Allele: G	Alternative Allele: A,T
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.97, A: 0.03, others allele: 0.00, population size: 116. )

Flanking Sequence (100 bp) in Reference Genome:

TAGTCTTTTGAGTTGTGTAGGCTTAGGATCTAAAGTTGTGATTCTGGTTGGGTCTGTGGTAGAGCAGGTCCAATGTAACCTGAGTGACCTACGATTGGTG[G/A,T]
GCTGAACTGTGCACTCTAACAATTACGCTGACTATACTGATTATGCTGTTAATTATATACCGAGCTCGAGCGAACAGCCTGTGAGCTTTTATACTAGTTA

Reverse complement sequence

TAACTAGTATAAAAGCTCACAGGCTGTTCGCTCGAGCTCGGTATATAATTAACAGCATAATCAGTATAGTCAGCGTAATTGTTAGAGTGCACAGTTCAGC[C/T,A]
CACCAATCGTAGGTCACTCAGGTTACATTGGACCTGCTCTACCACAGACCCAACCAGAATCACAACTTTAGATCCTAAGCCTACACAACTCAAAAGACTA

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	90.30%	9.70%	0.04%	0.00%	T: 0.02%
All Indica	2759	92.00%	8.00%	0.00%	0.00%	NA
All Japonica	1512	95.00%	4.80%	0.13%	0.00%	NA
Aus	269	44.20%	55.80%	0.00%	0.00%	NA
Indica I	595	98.80%	1.20%	0.00%	0.00%	NA
Indica II	465	99.40%	0.60%	0.00%	0.00%	NA
Indica III	913	87.50%	12.50%	0.00%	0.00%	NA
Indica Intermediate	786	87.70%	12.30%	0.00%	0.00%	NA
Temperate Japonica	767	99.90%	0.00%	0.13%	0.00%	NA
Tropical Japonica	504	86.30%	13.70%	0.00%	0.00%	NA
Japonica Intermediate	241	97.90%	1.70%	0.41%	0.00%	NA
VI/Aromatic	96	96.90%	2.10%	0.00%	0.00%	T: 1.04%
Intermediate	90	87.80%	12.20%	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
vg1001428076	G -> T	LOC_Os10g03360.1	upstream_gene_variant ; 3066.0bp to feature; MODIFIER	silent_mutation	Average:53.988; most accessible tissue: Zhenshan97 panicle, score: 63.607	N	N	N	N
vg1001428076	G -> T	LOC_Os10g03350.1	downstream_gene_variant ; 4303.0bp to feature; MODIFIER	silent_mutation	Average:53.988; most accessible tissue: Zhenshan97 panicle, score: 63.607	N	N	N	N
vg1001428076	G -> T	LOC_Os10g03350-LOC_Os10g03360	intergenic_region ; MODIFIER	silent_mutation	Average:53.988; most accessible tissue: Zhenshan97 panicle, score: 63.607	N	N	N	N
vg1001428076	G -> A	LOC_Os10g03360.1	upstream_gene_variant ; 3066.0bp to feature; MODIFIER	silent_mutation	Average:53.988; most accessible tissue: Zhenshan97 panicle, score: 63.607	N	N	N	N
vg1001428076	G -> A	LOC_Os10g03350.1	downstream_gene_variant ; 4303.0bp to feature; MODIFIER	silent_mutation	Average:53.988; most accessible tissue: Zhenshan97 panicle, score: 63.607	N	N	N	N
vg1001428076	G -> A	LOC_Os10g03350-LOC_Os10g03360	intergenic_region ; MODIFIER	silent_mutation	Average:53.988; most accessible tissue: Zhenshan97 panicle, score: 63.607	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1001428076	2.13E-11	NA	mr1486	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
vg1001428076	6.00E-11	NA	mr1548	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
vg1001428076	4.55E-07	NA	mr1588	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
vg1001428076	2.70E-12	NA	mr1486_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
vg1001428076	3.17E-12	NA	mr1588_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