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Detailed information for vg0335284080:

Variant ID: vg0335284080 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 35284080
Reference Allele: G	Alternative Allele: T
Primary Allele: G	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CTGTTCACTTTGATGCTATTTTCAACCTTACCAAATTTTGGTAAAGTTGTTAAAAAAGTGGCTACATTTAGTTTGCTGCCAAATTTTGCTAACTATATAA[G/T]
AAATCATGCCAAAATTTTGGCAAGTTGCCAAACTTTTAGTAACTATGCCAAAATTTTGGCAATGCCAAAATTTAGTAAGGTTTTTTTTTGCAACAAAGTG

Reverse complement sequence

CACTTTGTTGCAAAAAAAAACCTTACTAAATTTTGGCATTGCCAAAATTTTGGCATAGTTACTAAAAGTTTGGCAACTTGCCAAAATTTTGGCATGATTT[C/A]
TTATATAGTTAGCAAAATTTGGCAGCAAACTAAATGTAGCCACTTTTTTAACAACTTTACCAAAATTTGGTAAGGTTGAAAATAGCATCAAAGTGAACAG

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	95.40%	3.20%	1.42%	0.00%	NA
All Indica	2759	99.10%	0.00%	0.87%	0.00%	NA
All Japonica	1512	88.20%	9.30%	2.51%	0.00%	NA
Aus	269	98.90%	0.00%	1.12%	0.00%	NA
Indica I	595	96.10%	0.00%	3.87%	0.00%	NA
Indica II	465	100.00%	0.00%	0.00%	0.00%	NA
Indica III	913	99.90%	0.10%	0.00%	0.00%	NA
Indica Intermediate	786	99.90%	0.00%	0.13%	0.00%	NA
Temperate Japonica	767	97.10%	1.20%	1.69%	0.00%	NA
Tropical Japonica	504	73.40%	23.40%	3.17%	0.00%	NA
Japonica Intermediate	241	90.50%	5.80%	3.73%	0.00%	NA
VI/Aromatic	96	94.80%	4.20%	1.04%	0.00%	NA
Intermediate	90	92.20%	6.70%	1.11%	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
vg0335284080	G -> T	LOC_Os03g62280.1	upstream_gene_variant ; 918.0bp to feature; MODIFIER	silent_mutation	Average:40.209; most accessible tissue: Minghui63 panicle, score: 62.157	N	N	N	N
vg0335284080	G -> T	LOC_Os03g62280.2	upstream_gene_variant ; 918.0bp to feature; MODIFIER	silent_mutation	Average:40.209; most accessible tissue: Minghui63 panicle, score: 62.157	N	N	N	N
vg0335284080	G -> T	LOC_Os03g62290.1	downstream_gene_variant ; 4550.0bp to feature; MODIFIER	silent_mutation	Average:40.209; most accessible tissue: Minghui63 panicle, score: 62.157	N	N	N	N
vg0335284080	G -> T	LOC_Os03g62270-LOC_Os03g62280	intergenic_region ; MODIFIER	silent_mutation	Average:40.209; most accessible tissue: Minghui63 panicle, score: 62.157	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0335284080	2.32E-06	2.99E-08	mr1422_2	Jap_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
vg0335284080	NA	7.60E-06	mr1873_2	Jap_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
vg0335284080	4.69E-07	NA	mr1916_2	Jap_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