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Detailed information for vg0629086139:

Variant ID: vg0629086139 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 29086139
Reference Allele: G	Alternative Allele: T
Primary Allele: G	Secondary Allele: T

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 123. )

Flanking Sequence (100 bp) in Reference Genome:

CACGCCCGGTGGGACCCATTAGGAGTCAGAAATTAATCTTCCTCATGGCCGAGAAGCTGCCACCGTCGCCATCCTCGGCTAGCCCAGGTACTGTTAAAGA[G/T]
AAAATCCAAATACTAGGTTTGAGCGAAGTTAATGAAGGGAATATTGTGGCTATTGATCCGGAAAAGCTCACACCTGACCAGAAGAAGGATTTCGAAGCAA

Reverse complement sequence

TTGCTTCGAAATCCTTCTTCTGGTCAGGTGTGAGCTTTTCCGGATCAATAGCCACAATATTCCCTTCATTAACTTCGCTCAAACCTAGTATTTGGATTTT[C/A]
TCTTTAACAGTACCTGGGCTAGCCGAGGATGGCGACGGTGGCAGCTTCTCGGCCATGAGGAAGATTAATTTCTGACTCCTAATGGGTCCCACCGGGCGTG

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	92.50%	7.30%	0.19%	0.00%	NA
All Indica	2759	87.60%	12.10%	0.29%	0.00%	NA
All Japonica	1512	99.70%	0.30%	0.07%	0.00%	NA
Aus	269	99.30%	0.70%	0.00%	0.00%	NA
Indica I	595	98.80%	1.00%	0.17%	0.00%	NA
Indica II	465	85.60%	13.80%	0.65%	0.00%	NA
Indica III	913	81.70%	18.30%	0.00%	0.00%	NA
Indica Intermediate	786	87.00%	12.50%	0.51%	0.00%	NA
Temperate Japonica	767	99.70%	0.30%	0.00%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	98.80%	0.80%	0.41%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	96.70%	3.30%	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
vg0629086139	G -> T	LOC_Os06g48070.1	intron_variant ; MODIFIER	silent_mutation	Average:29.643; most accessible tissue: Minghui63 root, score: 52.955	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0629086139	1.95E-06	1.59E-08	mr1090	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
vg0629086139	7.69E-07	2.32E-08	mr1211	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
vg0629086139	NA	5.77E-08	mr1090_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
vg0629086139	NA	1.41E-08	mr1211_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