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Detailed information for vg0142148398:

Variant ID: vg0142148398 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 42148398
Reference Allele: T	Alternative Allele: A
Primary Allele: T	Secondary Allele: A

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.97, A: 0.03, others allele: 0.00, population size: 92. )

Flanking Sequence (100 bp) in Reference Genome:

GTCTAATAAATGTATATATCTGAACACAAATCAGTTTTATTTATGGTTTATAACTAATATATTTTTTACTTTTAGCTCAATTATTAAAAATATTAAAAGT[T/A]
ACTAGTTAGAAATTTTCACAGCAAAGCACGGGGAAGGTTGTTCTTAATAGATAAAAACCCAGACTACTCTGAAAAAGCACAAACCCTCCAACACTGCCTT

Reverse complement sequence

AAGGCAGTGTTGGAGGGTTTGTGCTTTTTCAGAGTAGTCTGGGTTTTTATCTATTAAGAACAACCTTCCCCGTGCTTTGCTGTGAAAATTTCTAACTAGT[A/T]
ACTTTTAATATTTTTAATAATTGAGCTAAAAGTAAAAAATATATTAGTTATAAACCATAAATAAAACTGATTTGTGTTCAGATATATACATTTATTAGAC

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	78.10%	19.90%	0.23%	1.78%	NA
All Indica	2759	66.10%	33.40%	0.11%	0.40%	NA
All Japonica	1512	94.00%	0.70%	0.53%	4.76%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	57.50%	41.20%	0.34%	1.01%	NA
Indica II	465	89.00%	11.00%	0.00%	0.00%	NA
Indica III	913	55.20%	44.80%	0.00%	0.00%	NA
Indica Intermediate	786	71.80%	27.50%	0.13%	0.64%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	83.30%	2.00%	1.19%	13.49%	NA
Japonica Intermediate	241	97.50%	0.00%	0.83%	1.66%	NA
VI/Aromatic	96	97.90%	2.10%	0.00%	0.00%	NA
Intermediate	90	92.20%	6.70%	0.00%	1.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0142148398	T -> A	LOC_Os01g72650.1	upstream_gene_variant ; 1312.0bp to feature; MODIFIER	silent_mutation	Average:33.599; most accessible tissue: Zhenshan97 panicle, score: 52.263	N	N	N	N
vg0142148398	T -> A	LOC_Os01g72630-LOC_Os01g72650	intergenic_region ; MODIFIER	silent_mutation	Average:33.599; most accessible tissue: Zhenshan97 panicle, score: 52.263	N	N	N	N
vg0142148398	T -> DEL	N	N	silent_mutation	Average:33.599; most accessible tissue: Zhenshan97 panicle, score: 52.263	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0142148398	NA	1.15E-06	mr1014	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
vg0142148398	6.29E-06	1.27E-09	mr1015	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
vg0142148398	NA	3.49E-07	mr1274	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
vg0142148398	NA	3.58E-07	mr1274_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
vg0142148398	NA	1.97E-07	mr1274_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