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Detailed information for vg0104590396:

Variant ID: vg0104590396 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 4590396
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 268. )

Flanking Sequence (100 bp) in Reference Genome:

GTCAACGTGCCACGCCAGTGGAAACCACCATTGAAACTGCTAAGGCCTGGTTCGGTTTGGAGGGGATTAAGAGGGAATAATTCCACACCATAATAGGTGT[G/A]
GAATAAATCCCCTCCAATCCCTTTCTCATGGGGATTAACTGAACAAGGCTTAAGGGAGTTAAATTATACCAGTTTTAATAGTTAGAGGGTAAAGATATCA

Reverse complement sequence

TGATATCTTTACCCTCTAACTATTAAAACTGGTATAATTTAACTCCCTTAAGCCTTGTTCAGTTAATCCCCATGAGAAAGGGATTGGAGGGGATTTATTC[C/T]
ACACCTATTATGGTGTGGAATTATTCCCTCTTAATCCCCTCCAAACCGAACCAGGCCTTAGCAGTTTCAATGGTGGTTTCCACTGGCGTGGCACGTTGAC

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	91.20%	8.60%	0.19%	0.00%	NA
All Indica	2759	99.70%	0.30%	0.00%	0.00%	NA
All Japonica	1512	74.00%	25.50%	0.46%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	99.80%	0.20%	0.00%	0.00%	NA
Indica III	913	99.60%	0.40%	0.00%	0.00%	NA
Indica Intermediate	786	99.60%	0.40%	0.00%	0.00%	NA
Temperate Japonica	767	96.00%	3.50%	0.52%	0.00%	NA
Tropical Japonica	504	50.60%	48.80%	0.60%	0.00%	NA
Japonica Intermediate	241	53.10%	46.90%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	85.60%	12.20%	2.22%	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
vg0104590396	G -> A	LOC_Os01g09140.1	upstream_gene_variant ; 524.0bp to feature; MODIFIER	silent_mutation	Average:78.367; most accessible tissue: Zhenshan97 root, score: 87.822	N	N	N	N
vg0104590396	G -> A	LOC_Os01g09130.1	downstream_gene_variant ; 2561.0bp to feature; MODIFIER	silent_mutation	Average:78.367; most accessible tissue: Zhenshan97 root, score: 87.822	N	N	N	N
vg0104590396	G -> A	LOC_Os01g09130-LOC_Os01g09140	intergenic_region ; MODIFIER	silent_mutation	Average:78.367; most accessible tissue: Zhenshan97 root, score: 87.822	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0104590396	1.92E-07	NA	mr1023	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
vg0104590396	2.26E-06	NA	mr1142	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
vg0104590396	2.99E-08	NA	mr1489	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
vg0104590396	1.19E-08	NA	mr1778	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
vg0104590396	NA	1.11E-06	mr1554_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
vg0104590396	NA	2.74E-07	mr1566_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
vg0104590396	NA	2.27E-13	mr1769_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
vg0104590396	NA	4.87E-14	mr1769_2	Jap_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