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Detailed information for vg0101949130:

Variant ID: vg0101949130 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 1949130
Reference Allele: T	Alternative Allele: G
Primary Allele: G	Secondary Allele: T

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.96, G: 0.04, others allele: 0.00, population size: 120. )

Flanking Sequence (100 bp) in Reference Genome:

ACCTCAGGCTTCTTGACCTCGGCCTTGGGCACGGTGACAGTGAGCACGCCGTTCTCCAGTCCGGCCTTCACCTGGTCCACCTTGGCGTTCTCCGGCAGCC[T/G]
GAACCGCCGCATGAACTGCCCGCTGCTGCGCTCCACGCGGTGCCACTTGTCGTTCTTGTCCTCCTTCTCCTTGCTGCGCTGGCCGCTGATCACCAGCACG

Reverse complement sequence

CGTGCTGGTGATCAGCGGCCAGCGCAGCAAGGAGAAGGAGGACAAGAACGACAAGTGGCACCGCGTGGAGCGCAGCAGCGGGCAGTTCATGCGGCGGTTC[A/C]
GGCTGCCGGAGAACGCCAAGGTGGACCAGGTGAAGGCCGGACTGGAGAACGGCGTGCTCACTGTCACCGTGCCCAAGGCCGAGGTCAAGAAGCCTGAGGT

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	51.10%	47.80%	1.04%	0.00%	NA
All Indica	2759	75.10%	23.20%	1.63%	0.00%	NA
All Japonica	1512	8.20%	91.60%	0.20%	0.00%	NA
Aus	269	63.90%	36.10%	0.00%	0.00%	NA
Indica I	595	35.00%	60.20%	4.87%	0.00%	NA
Indica II	465	93.50%	5.80%	0.65%	0.00%	NA
Indica III	913	87.60%	12.30%	0.11%	0.00%	NA
Indica Intermediate	786	80.20%	18.30%	1.53%	0.00%	NA
Temperate Japonica	767	14.60%	85.30%	0.13%	0.00%	NA
Tropical Japonica	504	1.80%	97.80%	0.40%	0.00%	NA
Japonica Intermediate	241	1.20%	98.80%	0.00%	0.00%	NA
VI/Aromatic	96	6.20%	93.80%	0.00%	0.00%	NA
Intermediate	90	45.60%	53.30%	1.11%	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
vg0101949130	T -> G	LOC_Os01g04370.1	synonymous_variant ; p.Arg110Arg; LOW	synonymous_codon	Average:66.755; most accessible tissue: Zhenshan97 flower, score: 86.841	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0101949130	NA	2.52E-08	mr1184_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
vg0101949130	NA	2.33E-07	mr1278_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
vg0101949130	NA	3.56E-06	mr1329_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
vg0101949130	NA	6.79E-07	mr1418_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
vg0101949130	NA	2.16E-06	mr1488_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
vg0101949130	NA	2.88E-07	mr1524_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
vg0101949130	NA	2.25E-09	mr1683_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
vg0101949130	NA	5.22E-13	mr1838_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
vg0101949130	NA	7.10E-06	mr1982_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