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Detailed information for vg1210984536:

Variant ID: vg1210984536 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 10984536
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: 97. )

Flanking Sequence (100 bp) in Reference Genome:

ACAAAGGAATCAACTGAGAATCAAATTAAACAAATGAATCAAATGAATCGCAGGCTCGATCATTTGCAGCAATGGCAGATTTGGACTTGTTGGATCAATC[G/A]
ATCTCAAGGCATCCACGCACTCGTCCACACGACAGGCTGCTCCTTCCATGCAAGGAATGCTCCGGCAGCGGCAGCGTTGTCCATGTCACTGCCGTAGTCC

Reverse complement sequence

GGACTACGGCAGTGACATGGACAACGCTGCCGCTGCCGGAGCATTCCTTGCATGGAAGGAGCAGCCTGTCGTGTGGACGAGTGCGTGGATGCCTTGAGAT[C/T]
GATTGATCCAACAAGTCCAAATCTGCCATTGCTGCAAATGATCGAGCCTGCGATTCATTTGATTCATTTGTTTAATTTGATTCTCAGTTGATTCCTTTGT

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	90.00%	9.90%	0.02%	0.00%	NA
All Indica	2759	83.30%	16.70%	0.04%	0.00%	NA
All Japonica	1512	99.70%	0.30%	0.00%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	55.10%	44.90%	0.00%	0.00%	NA
Indica II	465	94.60%	5.20%	0.22%	0.00%	NA
Indica III	913	93.10%	6.90%	0.00%	0.00%	NA
Indica Intermediate	786	86.50%	13.50%	0.00%	0.00%	NA
Temperate Japonica	767	99.70%	0.30%	0.00%	0.00%	NA
Tropical Japonica	504	99.40%	0.60%	0.00%	0.00%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	94.40%	5.60%	0.00%	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
vg1210984536	G -> A	LOC_Os12g18930.1	synonymous_variant ; p.Ser10Ser; LOW	synonymous_codon	Average:64.408; most accessible tissue: Minghui63 young leaf, score: 77.654	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1210984536	NA	7.80E-06	mr1308	Ind_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
vg1210984536	NA	5.28E-06	mr1164_2	Ind_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
vg1210984536	NA	6.31E-07	mr1170_2	Ind_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
vg1210984536	NA	2.59E-07	mr1215_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
vg1210984536	NA	5.81E-09	mr1220_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
vg1210984536	5.33E-07	NA	mr1308_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
vg1210984536	2.92E-07	1.33E-09	mr1308_2	Ind_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
vg1210984536	1.28E-06	NA	mr1361_2	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
vg1210984536	7.80E-07	6.06E-10	mr1361_2	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
vg1210984536	NA	4.40E-07	mr1745_2	Ind_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
vg1210984536	5.54E-06	5.53E-06	mr1853_2	Ind_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