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Detailed information for vg0110094967:

Variant ID: vg0110094967 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 10094967
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GCCTAATGTTTCGGCATTGCTCTGTGGTGTGCGAAGAGCGTCCGTGAAAGGCGCAGTAGAGGTCTTTTCGGACCTTCTTACGGGCTGGCTGCTGATGGTT[G/A]
CTCGCTTGTTGGGCATCAAACTCCTTGCGGAGGGCTTGCACTTCTTCGACCGCCATCACAGCTTTGCCCGCACAGTCTGTTCTGAACTTTCTCCAAGTTA

Reverse complement sequence

TAACTTGGAGAAAGTTCAGAACAGACTGTGCGGGCAAAGCTGTGATGGCGGTCGAAGAAGTGCAAGCCCTCCGCAAGGAGTTTGATGCCCAACAAGCGAG[C/T]
AACCATCAGCAGCCAGCCCGTAAGAAGGTCCGAAAAGACCTCTACTGCGCCTTTCACGGACGCTCTTCGCACACCACAGAGCAATGCCGAAACATTAGGC

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	50.30%	32.70%	16.97%	0.00%	NA
All Indica	2759	21.30%	50.70%	27.98%	0.00%	NA
All Japonica	1512	97.00%	2.40%	0.60%	0.00%	NA
Aus	269	95.20%	3.70%	1.12%	0.00%	NA
Indica I	595	12.10%	48.40%	39.50%	0.00%	NA
Indica II	465	21.70%	48.20%	30.11%	0.00%	NA
Indica III	913	26.50%	51.20%	22.34%	0.00%	NA
Indica Intermediate	786	21.90%	53.60%	24.55%	0.00%	NA
Temperate Japonica	767	98.30%	1.20%	0.52%	0.00%	NA
Tropical Japonica	504	95.20%	4.20%	0.60%	0.00%	NA
Japonica Intermediate	241	96.30%	2.90%	0.83%	0.00%	NA
VI/Aromatic	96	20.80%	68.80%	10.42%	0.00%	NA
Intermediate	90	54.40%	36.70%	8.89%	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
vg0110094967	G -> A	LOC_Os01g18040.1	synonymous_variant ; p.Ser656Ser; LOW	synonymous_codon	Average:22.242; most accessible tissue: Callus, score: 37.602	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0110094967	6.20E-06	NA	mr1002	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
vg0110094967	NA	1.98E-17	mr1913	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
vg0110094967	NA	3.62E-06	mr1875_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