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Detailed information for vg0621626147:

Variant ID: vg0621626147 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 21626147
Reference Allele: G	Alternative Allele: T
Primary Allele: G	Secondary Allele: T

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.95, T: 0.05, others allele: 0.00, population size: 113. )

Flanking Sequence (100 bp) in Reference Genome:

ACCAGTTGGTCTATTCGAGGAAGAGGGAAGTGATCCTTGGGACACGCCTTGTTGAGGTCGGTGAAATCGATACACATTCTCCATTTCCCGTTGGCCTTCC[G/T]
CACCATGAATGGGTTGGCTAGCCACTCTGGATGGAGTACCTCTCTGATGAAACCAGCTTTGAGAAGCTTGTCGAGCTCTTCTCGTATGGCTTGTTTTTGA

Reverse complement sequence

TCAAAAACAAGCCATACGAGAAGAGCTCGACAAGCTTCTCAAAGCTGGTTTCATCAGAGAGGTACTCCATCCAGAGTGGCTAGCCAACCCATTCATGGTG[C/A]
GGAAGGCCAACGGGAAATGGAGAATGTGTATCGATTTCACCGACCTCAACAAGGCGTGTCCCAAGGATCACTTCCCTCTTCCTCGAATAGACCAACTGGT

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	77.40%	20.80%	1.82%	0.00%	NA
All Indica	2759	77.30%	21.90%	0.87%	0.00%	NA
All Japonica	1512	94.70%	5.00%	0.33%	0.00%	NA
Aus	269	2.60%	96.30%	1.12%	0.00%	NA
Indica I	595	94.50%	4.90%	0.67%	0.00%	NA
Indica II	465	83.20%	16.30%	0.43%	0.00%	NA
Indica III	913	64.00%	35.00%	0.99%	0.00%	NA
Indica Intermediate	786	76.20%	22.60%	1.15%	0.00%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	85.90%	13.90%	0.20%	0.00%	NA
Japonica Intermediate	241	96.30%	2.10%	1.66%	0.00%	NA
VI/Aromatic	96	13.50%	34.40%	52.08%	0.00%	NA
Intermediate	90	82.20%	13.30%	4.44%	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
vg0621626147	G -> T	LOC_Os06g36730.1	synonymous_variant ; p.Arg912Arg; LOW	synonymous_codon	Average:38.294; most accessible tissue: Zhenshan97 flag leaf, score: 70.837	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0621626147	7.92E-06	NA	mr1164	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
vg0621626147	NA	8.47E-06	mr1215	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
vg0621626147	6.35E-06	NA	mr1434	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
vg0621626147	7.04E-06	4.07E-06	mr1434	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
vg0621626147	2.61E-06	NA	mr1881	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
vg0621626147	NA	5.96E-06	mr1522_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