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Detailed information for vg0142373253:

Variant ID: vg0142373253 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 42373253
Reference Allele: T	Alternative Allele: A
Primary Allele: T	Secondary Allele: A

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.68, T: 0.32, others allele: 0.00, population size: 72. )

Flanking Sequence (100 bp) in Reference Genome:

AAACTAGGTATATTTTGCACTGAGGGCAAAATAGTCATTATTAAAAAAATAACGGTTGTAACGGTGTGGAGTTGACAGTGATGGCATTTTTGGGAGAAAG[T/A]
GGCTTGTGCAATGGCATTTTTGGAAAGTTGTCTTTGTCGATGGCATTTCTGGGATTAGGGTGCTTGTTGATGGCATTTTATGGATTTTCTCTTAATTTAA

Reverse complement sequence

TTAAATTAAGAGAAAATCCATAAAATGCCATCAACAAGCACCCTAATCCCAGAAATGCCATCGACAAAGACAACTTTCCAAAAATGCCATTGCACAAGCC[A/T]
CTTTCTCCCAAAAATGCCATCACTGTCAACTCCACACCGTTACAACCGTTATTTTTTTAATAATGACTATTTTGCCCTCAGTGCAAAATATACCTAGTTT

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	61.60%	22.20%	0.61%	15.68%	NA
All Indica	2759	62.20%	17.10%	0.54%	20.12%	NA
All Japonica	1512	56.30%	35.10%	0.60%	8.00%	NA
Aus	269	78.80%	2.60%	0.74%	17.84%	NA
Indica I	595	71.30%	28.60%	0.17%	0.00%	NA
Indica II	465	25.20%	5.60%	0.22%	69.03%	NA
Indica III	913	71.50%	15.80%	0.88%	11.83%	NA
Indica Intermediate	786	66.50%	16.80%	0.64%	16.03%	NA
Temperate Japonica	767	77.70%	21.10%	0.78%	0.39%	NA
Tropical Japonica	504	27.40%	49.80%	0.40%	22.42%	NA
Japonica Intermediate	241	48.50%	49.00%	0.41%	2.07%	NA
VI/Aromatic	96	76.00%	20.80%	0.00%	3.12%	NA
Intermediate	90	62.20%	18.90%	3.33%	15.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0142373253	T -> A	LOC_Os01g73040.1	upstream_gene_variant ; 3941.0bp to feature; MODIFIER	silent_mutation	Average:42.998; most accessible tissue: Zhenshan97 panicle, score: 82.888	N	N	N	N
vg0142373253	T -> A	LOC_Os01g73024.1	downstream_gene_variant ; 2888.0bp to feature; MODIFIER	silent_mutation	Average:42.998; most accessible tissue: Zhenshan97 panicle, score: 82.888	N	N	N	N
vg0142373253	T -> A	LOC_Os01g73024-LOC_Os01g73040	intergenic_region ; MODIFIER	silent_mutation	Average:42.998; most accessible tissue: Zhenshan97 panicle, score: 82.888	N	N	N	N
vg0142373253	T -> DEL	N	N	silent_mutation	Average:42.998; most accessible tissue: Zhenshan97 panicle, score: 82.888	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0142373253	5.30E-06	5.30E-06	mr1193	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
vg0142373253	NA	9.66E-07	mr1974	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
vg0142373253	2.82E-06	NA	mr1193_2	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
vg0142373253	NA	8.49E-07	mr1322_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
vg0142373253	NA	6.01E-07	mr1336_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