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Detailed information for vg0220340205:

Variant ID: vg0220340205 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 20340205
Reference Allele: A	Alternative Allele: G
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, A: 0.00, others allele: 0.00, population size: 213. )

Flanking Sequence (100 bp) in Reference Genome:

TGACATGTTCATGTGTATGTTCAGTTTGTTCTGGTGGTGTGATTGAACTGGGAATTACTTTAGAGGGTTGGCTCGAACTACTATGTGTATCCTTCATTGG[A/G]
AAAAAGCTCTCAAAGAAGGTAGCATCACGAGACTCCATAATTGTACCAACATGCATGTCAGGTACCTCAGATTTAACTATTAAAAATCTATAGGCAATGC

Reverse complement sequence

GCATTGCCTATAGATTTTTAATAGTTAAATCTGAGGTACCTGACATGCATGTTGGTACAATTATGGAGTCTCGTGATGCTACCTTCTTTGAGAGCTTTTT[T/C]
CCAATGAAGGATACACATAGTAGTTCGAGCCAACCCTCTAAAGTAATTCCCAGTTCAATCACACCACCAGAACAAACTGAACATACACATGAACATGTCA

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	77.30%	22.30%	0.32%	0.00%	NA
All Indica	2759	95.80%	3.90%	0.25%	0.00%	NA
All Japonica	1512	38.80%	60.80%	0.40%	0.00%	NA
Aus	269	99.60%	0.40%	0.00%	0.00%	NA
Indica I	595	98.50%	0.80%	0.67%	0.00%	NA
Indica II	465	90.80%	9.00%	0.22%	0.00%	NA
Indica III	913	96.70%	3.20%	0.11%	0.00%	NA
Indica Intermediate	786	95.80%	4.10%	0.13%	0.00%	NA
Temperate Japonica	767	20.90%	78.60%	0.52%	0.00%	NA
Tropical Japonica	504	53.40%	46.40%	0.20%	0.00%	NA
Japonica Intermediate	241	65.10%	34.40%	0.41%	0.00%	NA
VI/Aromatic	96	99.00%	1.00%	0.00%	0.00%	NA
Intermediate	90	68.90%	28.90%	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
vg0220340205	A -> G	LOC_Os02g34040.1	synonymous_variant ; p.Phe671Phe; LOW	synonymous_codon	Average:24.248; most accessible tissue: Minghui63 young leaf, score: 44.63	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0220340205	4.00E-06	3.99E-06	mr1293_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
vg0220340205	4.86E-06	4.86E-06	mr1497_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
vg0220340205	NA	5.93E-06	mr1738_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
vg0220340205	NA	5.21E-06	mr1851_2	Jap_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