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Detailed information for vg0221671440:

Variant ID: vg0221671440 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 21671440
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: 85. )

Flanking Sequence (100 bp) in Reference Genome:

AGGCACGGCTTCAGCCCACTTGATGAAGTAATCCGTAGCAACAAGCACGAACCTATGCCCCTTTGATGACGAAGGATAAATTTGACCAATGAAATCCAAA[G/T]
CCCATCCTCGGAACGGCCATAGTTTGATTATAGGGTTCAACACGGCGGCGGGCGCCAATTAAACATTGCCGAACCGTTGACAAGCCTCGCATCCCCTATA

Reverse complement sequence

TATAGGGGATGCGAGGCTTGTCAACGGTTCGGCAATGTTTAATTGGCGCCCGCCGCCGTGTTGAACCCTATAATCAAACTATGGCCGTTCCGAGGATGGG[C/A]
TTTGGATTTCATTGGTCAAATTTATCCTTCGTCATCAAAGGGGCATAGGTTCGTGCTTGTTGCTACGGATTACTTCATCAAGTGGGCTGAAGCCGTGCCT

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	44.30%	4.00%	34.13%	17.65%	NA
All Indica	2759	16.50%	5.30%	49.69%	28.56%	NA
All Japonica	1512	95.40%	0.00%	2.45%	2.18%	NA
Aus	269	18.20%	14.50%	66.91%	0.37%	NA
Indica I	595	15.00%	3.50%	31.26%	50.25%	NA
Indica II	465	11.20%	1.30%	56.56%	30.97%	NA
Indica III	913	18.10%	8.90%	59.80%	13.25%	NA
Indica Intermediate	786	18.80%	4.80%	47.84%	28.50%	NA
Temperate Japonica	767	98.70%	0.00%	0.65%	0.65%	NA
Tropical Japonica	504	90.30%	0.00%	5.16%	4.56%	NA
Japonica Intermediate	241	95.40%	0.00%	2.49%	2.07%	NA
VI/Aromatic	96	91.70%	0.00%	8.33%	0.00%	NA
Intermediate	90	65.60%	2.20%	18.89%	13.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0221671440	G -> T	LOC_Os02g36040.1	downstream_gene_variant ; 3644.0bp to feature; MODIFIER	silent_mutation	Average:10.606; most accessible tissue: Callus, score: 34.402	N	N	N	N
vg0221671440	G -> T	LOC_Os02g36060.1	downstream_gene_variant ; 4903.0bp to feature; MODIFIER	silent_mutation	Average:10.606; most accessible tissue: Callus, score: 34.402	N	N	N	N
vg0221671440	G -> T	LOC_Os02g36050.1	intron_variant ; MODIFIER	silent_mutation	Average:10.606; most accessible tissue: Callus, score: 34.402	N	N	N	N
vg0221671440	G -> DEL	N	N	silent_mutation	Average:10.606; most accessible tissue: Callus, score: 34.402	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0221671440	7.04E-07	1.61E-06	mr1005	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
vg0221671440	9.59E-06	NA	mr1012	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