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Detailed information for vg1214567309:

Variant ID: vg1214567309 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 14567309
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.99, others allele: 0.00, population size: 126. )

Flanking Sequence (100 bp) in Reference Genome:

AGGACTTAGACCTAGAACTTGGGATGATATGAAACGTACAATGAGGTCTAGATTTGTTCCTTCTTACTATGCTTGTGACATGTTAAATAAACTGCAACTT[T/C]
TAAGACAAGGTCCCAATTCTGTAGAAACATACTATCAAGAGATGATGATTGCTTTGTCATGCTGTGATTTGCAAGAAACTGAGGATGCTAGAATTTCTAG

Reverse complement sequence

CTAGAAATTCTAGCATCCTCAGTTTCTTGCAAATCACAGCATGACAAAGCAATCATCATCTCTTGATAGTATGTTTCTACAGAATTGGGACCTTGTCTTA[A/G]
AAGTTGCAGTTTATTTAACATGTCACAAGCATAGTAAGAAGGAACAAATCTAGACCTCATTGTACGTTTCATATCATCCCAAGTTCTAGGTCTAAGTCCT

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	91.00%	8.80%	0.19%	0.00%	NA
All Indica	2759	85.10%	14.60%	0.29%	0.00%	NA
All Japonica	1512	99.40%	0.50%	0.07%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	53.40%	46.10%	0.50%	0.00%	NA
Indica II	465	95.50%	4.50%	0.00%	0.00%	NA
Indica III	913	98.90%	0.70%	0.44%	0.00%	NA
Indica Intermediate	786	87.00%	12.80%	0.13%	0.00%	NA
Temperate Japonica	767	99.60%	0.30%	0.13%	0.00%	NA
Tropical Japonica	504	99.20%	0.80%	0.00%	0.00%	NA
Japonica Intermediate	241	99.20%	0.80%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	95.60%	4.40%	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
vg1214567309	T -> C	LOC_Os12g25300.1	splice_region_variant&intron_variant ; LOW	silent_mutation	Average:12.027; most accessible tissue: Zhenshan97 flag leaf, score: 22.512	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1214567309	NA	6.82E-07	mr1063_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
vg1214567309	NA	2.80E-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
vg1214567309	NA	1.96E-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
vg1214567309	NA	2.55E-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
vg1214567309	NA	1.06E-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
vg1214567309	NA	3.73E-06	mr1220_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
vg1214567309	NA	1.86E-06	mr1227_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
vg1214567309	NA	2.49E-07	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
vg1214567309	NA	4.83E-07	mr1361_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
vg1214567309	9.21E-06	9.21E-06	mr1529_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
vg1214567309	NA	1.79E-06	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
vg1214567309	NA	5.92E-06	mr1887_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