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Detailed information for vg0430364870:

Variant ID: vg0430364870 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 30364870
Reference Allele: T	Alternative Allele: A
Primary Allele: A	Secondary Allele: T

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.82, A: 0.18, others allele: 0.00, population size: 78. )

Flanking Sequence (100 bp) in Reference Genome:

TCCTTCCAAACTGGACTTTTCCTCTCTTCATAAATGGACGGAAATCGGTATGGTTGCTGTCCTAGTGCGCCAGATGACGGGACGGCCCATACCTACCCCC[T/A]
CTTCCGCCGGAAGCAGGTGCGACGTGGGATTATGGCTGTCCGTTGCTGACGCGACCAGTGTCAGACCGGTCACAGATCGGTCATTCTTGTCCTCCACGCG

Reverse complement sequence

CGCGTGGAGGACAAGAATGACCGATCTGTGACCGGTCTGACACTGGTCGCGTCAGCAACGGACAGCCATAATCCCACGTCGCACCTGCTTCCGGCGGAAG[A/T]
GGGGGTAGGTATGGGCCGTCCCGTCATCTGGCGCACTAGGACAGCAACCATACCGATTTCCGTCCATTTATGAAGAGAGGAAAAGTCCAGTTTGGAAGGA

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	56.60%	21.00%	6.33%	16.08%	NA
All Indica	2759	78.10%	1.30%	7.97%	12.58%	NA
All Japonica	1512	18.40%	59.90%	2.45%	19.31%	NA
Aus	269	47.60%	0.70%	10.41%	41.26%	NA
Indica I	595	82.90%	1.20%	8.07%	7.90%	NA
Indica II	465	55.10%	2.60%	15.70%	26.67%	NA
Indica III	913	89.20%	0.30%	3.29%	7.23%	NA
Indica Intermediate	786	75.40%	1.80%	8.78%	13.99%	NA
Temperate Japonica	767	3.50%	89.70%	1.04%	5.74%	NA
Tropical Japonica	504	42.50%	27.60%	4.17%	25.79%	NA
Japonica Intermediate	241	15.40%	32.40%	3.32%	48.96%	NA
VI/Aromatic	96	65.60%	29.20%	5.21%	0.00%	NA
Intermediate	90	54.40%	24.40%	10.00%	11.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0430364870	T -> DEL	N	N	silent_mutation	Average:15.012; most accessible tissue: Zhenshan97 flag leaf, score: 26.688	N	N	N	N
vg0430364870	T -> A	LOC_Os04g51240.1	upstream_gene_variant ; 1212.0bp to feature; MODIFIER	silent_mutation	Average:15.012; most accessible tissue: Zhenshan97 flag leaf, score: 26.688	N	N	N	N
vg0430364870	T -> A	LOC_Os04g51250.1	downstream_gene_variant ; 1059.0bp to feature; MODIFIER	silent_mutation	Average:15.012; most accessible tissue: Zhenshan97 flag leaf, score: 26.688	N	N	N	N
vg0430364870	T -> A	LOC_Os04g51240-LOC_Os04g51250	intergenic_region ; MODIFIER	silent_mutation	Average:15.012; most accessible tissue: Zhenshan97 flag leaf, score: 26.688	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0430364870	1.63E-06	1.40E-60	mr1241_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
vg0430364870	NA	1.23E-06	mr1509_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