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Detailed information for vg0114124547:

Variant ID: vg0114124547 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 14124547
Reference Allele: T	Alternative Allele: G
Primary Allele: T	Secondary Allele: G

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.96, G: 0.03, others allele: 0.00, population size: 182. )

Flanking Sequence (100 bp) in Reference Genome:

TATAATTGAAGACATGTCTTAGGGAAACATCCCGGAATACGGTGGCTCAGGTATAGAGAATGAAGGTATTGATTTTGATCTGGAAGATATGTTGCGGCAC[T/G]
TTGAACCAGAGGTCCTAACTGGTACAAGACGAGGGTTGGACAATTGGGAAGCGTTGGAAAAAGCAGCGAAGGAGCTTCTGTACGACGAAGCCAAAGGATG

Reverse complement sequence

CATCCTTTGGCTTCGTCGTACAGAAGCTCCTTCGCTGCTTTTTCCAACGCTTCCCAATTGTCCAACCCTCGTCTTGTACCAGTTAGGACCTCTGGTTCAA[A/C]
GTGCCGCAACATATCTTCCAGATCAAAATCAATACCTTCATTCTCTATACCTGAGCCACCGTATTCCGGGATGTTTCCCTAAGACATGTCTTCAATTATA

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	47.80%	45.20%	6.86%	0.06%	NA
All Indica	2759	25.40%	66.30%	8.23%	0.07%	NA
All Japonica	1512	95.40%	0.90%	3.70%	0.07%	NA
Aus	269	3.00%	89.20%	7.81%	0.00%	NA
Indica I	595	3.70%	86.90%	9.24%	0.17%	NA
Indica II	465	58.70%	35.70%	5.38%	0.22%	NA
Indica III	913	23.70%	69.10%	7.23%	0.00%	NA
Indica Intermediate	786	24.00%	65.60%	10.31%	0.00%	NA
Temperate Japonica	767	98.30%	0.00%	1.56%	0.13%	NA
Tropical Japonica	504	89.70%	2.00%	8.33%	0.00%	NA
Japonica Intermediate	241	97.90%	1.20%	0.83%	0.00%	NA
VI/Aromatic	96	51.00%	30.20%	18.75%	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
vg0114124547	T -> G	LOC_Os01g25040.1	missense_variant ; p.Phe308Val; MODERATE	nonsynonymous_codon ; F308V	Average:32.236; most accessible tissue: Minghui63 flag leaf, score: 58.568	unknown	unknown	TOLERATED	1.00
vg0114124547	T -> DEL	LOC_Os01g25040.1	N	frameshift_variant	Average:32.236; most accessible tissue: Minghui63 flag leaf, score: 58.568	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0114124547	NA	1.42E-11	Grain_thickness	Ind_All	Not	Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg0114124547	NA	5.65E-11	Grain_width	Ind_All	Not	Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg0114124547	NA	1.51E-11	mr1069	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
vg0114124547	NA	5.63E-13	mr1441	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
vg0114124547	NA	1.56E-06	mr1332_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
vg0114124547	NA	9.02E-06	mr1332_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
vg0114124547	NA	1.39E-07	mr1482_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
vg0114124547	NA	3.39E-11	mr1654_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
vg0114124547	NA	3.70E-07	mr1654_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
vg0114124547	NA	1.23E-10	mr1893_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