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Detailed information for vg0506631637:

Variant ID: vg0506631637 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 6631637
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: 309. )

Flanking Sequence (100 bp) in Reference Genome:

GTCAACAAGGGCAGGGGATGATGGAGAGAAACAAAGAAAATGCCGCCAAGAAGAAGTACCATCACCACTTGGGGTCAGGCGGCTATAGCATCGCAATGCC[G/A]
AAGTGGGAGGAGATGGAGGCAAGTTTGATTGAGAGGGGTATCGAACCGGCCAACGCTAAATGGCCGGATCGATCAAAGTTCTGGTACTATGCTCACGGTG

Reverse complement sequence

CACCGTGAGCATAGTACCAGAACTTTGATCGATCCGGCCATTTAGCGTTGGCCGGTTCGATACCCCTCTCAATCAAACTTGCCTCCATCTCCTCCCACTT[C/T]
GGCATTGCGATGCTATAGCCGCCTGACCCCAAGTGGTGATGGTACTTCTTCTTGGCGGCATTTTCTTTGTTTCTCTCCATCATCCCCTGCCCTTGTTGAC

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	95.60%	1.00%	3.34%	0.00%	NA
All Indica	2759	98.80%	0.20%	0.94%	0.00%	NA
All Japonica	1512	98.70%	1.30%	0.00%	0.00%	NA
Aus	269	44.20%	7.40%	48.33%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	98.30%	0.90%	0.86%	0.00%	NA
Indica III	913	99.30%	0.10%	0.55%	0.00%	NA
Indica Intermediate	786	97.70%	0.10%	2.16%	0.00%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	97.60%	2.40%	0.00%	0.00%	NA
Japonica Intermediate	241	96.70%	3.30%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	95.60%	2.20%	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
vg0506631637	G -> A	LOC_Os05g11680.1	upstream_gene_variant ; 4897.0bp to feature; MODIFIER	silent_mutation	Average:57.743; most accessible tissue: Minghui63 flag leaf, score: 74.563	N	N	N	N
vg0506631637	G -> A	LOC_Os05g11680-LOC_Os05g11700	intergenic_region ; MODIFIER	silent_mutation	Average:57.743; most accessible tissue: Minghui63 flag leaf, score: 74.563	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0506631637	1.82E-07	NA	mr1064	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
vg0506631637	NA	9.44E-07	mr1126	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
vg0506631637	NA	3.10E-08	mr1157	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
vg0506631637	NA	1.34E-09	mr1328	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
vg0506631637	NA	2.61E-09	mr1348	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
vg0506631637	NA	9.48E-08	mr1365	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
vg0506631637	NA	1.20E-09	mr1446	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
vg0506631637	5.08E-06	1.79E-15	mr1612	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
vg0506631637	NA	9.95E-07	mr1652	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
vg0506631637	NA	2.90E-08	mr1989	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