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Detailed information for vg0110176224:

Variant ID: vg0110176224 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 10176224
Reference Allele: A	Alternative Allele: G
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.61, A: 0.39, others allele: 0.00, population size: 90. )

Flanking Sequence (100 bp) in Reference Genome:

GAAAGTCGAAAGATACACTGGAAGCACGTAATGATCTGAAGCATATGGAACAACGCGGTGACCTTCACCCGGAACCAAAGGAGAAAGGAAGCCATTACTT[A/G]
AGTCCAGCCAGCTACACTCTTAGCAAGGCAGAGAAGGAAAGTATGTTTGAATGCTTGGAGAGCATCAAGGTACCGTCTGGATACTCCACGAATATAAAGC

Reverse complement sequence

GCTTTATATTCGTGGAGTATCCAGACGGTACCTTGATGCTCTCCAAGCATTCAAACATACTTTCCTTCTCTGCCTTGCTAAGAGTGTAGCTGGCTGGACT[T/C]
AAGTAATGGCTTCCTTTCTCCTTTGGTTCCGGGTGAAGGTCACCGCGTTGTTCCATATGCTTCAGATCATTACGTGCTTCCAGTGTATCTTTCGACTTTC

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	62.20%	35.10%	2.71%	0.00%	NA
All Indica	2759	91.60%	4.90%	3.44%	0.00%	NA
All Japonica	1512	3.20%	96.70%	0.13%	0.00%	NA
Aus	269	88.50%	3.00%	8.55%	0.00%	NA
Indica I	595	93.30%	4.40%	2.35%	0.00%	NA
Indica II	465	91.00%	3.90%	5.16%	0.00%	NA
Indica III	913	92.30%	4.20%	3.50%	0.00%	NA
Indica Intermediate	786	89.90%	6.90%	3.18%	0.00%	NA
Temperate Japonica	767	1.40%	98.60%	0.00%	0.00%	NA
Tropical Japonica	504	5.60%	94.20%	0.20%	0.00%	NA
Japonica Intermediate	241	3.70%	95.90%	0.41%	0.00%	NA
VI/Aromatic	96	85.40%	11.50%	3.12%	0.00%	NA
Intermediate	90	48.90%	45.60%	5.56%	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
vg0110176224	A -> G	LOC_Os01g18180.1	synonymous_variant ; p.Leu494Leu; LOW	synonymous_codon	Average:12.166; most accessible tissue: Minghui63 panicle, score: 20.733	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0110176224	NA	6.88E-13	mr1149	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
vg0110176224	NA	2.32E-09	mr1162	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
vg0110176224	5.00E-06	1.74E-16	mr1170	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
vg0110176224	3.43E-08	NA	mr1180	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
vg0110176224	4.25E-06	NA	mr1180	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
vg0110176224	3.65E-06	NA	mr1183	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
vg0110176224	4.56E-06	NA	mr1503	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
vg0110176224	NA	1.81E-10	mr1630	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
vg0110176224	NA	4.17E-10	mr1222_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