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Detailed information for vg0433246740:

Variant ID: vg0433246740 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 33246740
Reference Allele: A	Alternative Allele: T
Primary Allele: A	Secondary Allele: T

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.97, T: 0.02, others allele: 0.00, population size: 191. )

Flanking Sequence (100 bp) in Reference Genome:

CTTTCTATTTCATCGAACTTGCTTTGCATGGCTACATGGACCTGAGCTTGACTAATTGCATCTTTTTCCCCCTCTTGCTTCTGGACTTGGTACTTCAGAT[A/T]
AGTAAGAAAAAGATAATGTAAAAAAGTGATCATCTGTTACCGCTACTCGCGTGTTGGTTTCTGGTCGATTTCTCTATGTTTTCAGCAACCCAAACAGACA

Reverse complement sequence

TGTCTGTTTGGGTTGCTGAAAACATAGAGAAATCGACCAGAAACCAACACGCGAGTAGCGGTAACAGATGATCACTTTTTTACATTATCTTTTTCTTACT[T/A]
ATCTGAAGTACCAAGTCCAGAAGCAAGAGGGGGAAAAAGATGCAATTAGTCAAGCTCAGGTCCATGTAGCCATGCAAAGCAAGTTCGATGAAATAGAAAG

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	46.90%	7.30%	10.18%	35.63%	NA
All Indica	2759	26.70%	0.70%	13.74%	58.83%	NA
All Japonica	1512	87.40%	10.60%	0.53%	1.52%	NA
Aus	269	23.00%	53.50%	18.22%	5.20%	NA
Indica I	595	9.20%	0.70%	9.58%	80.50%	NA
Indica II	465	26.50%	0.20%	15.05%	58.28%	NA
Indica III	913	42.80%	0.10%	11.28%	45.78%	NA
Indica Intermediate	786	21.50%	1.70%	18.96%	57.89%	NA
Temperate Japonica	767	90.10%	9.60%	0.00%	0.26%	NA
Tropical Japonica	504	91.90%	3.60%	0.60%	3.97%	NA
Japonica Intermediate	241	69.30%	28.20%	2.07%	0.41%	NA
VI/Aromatic	96	51.00%	12.50%	34.38%	2.08%	NA
Intermediate	90	50.00%	12.20%	13.33%	24.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0433246740	A -> DEL	N	N	silent_mutation	Average:29.889; most accessible tissue: Minghui63 root, score: 60.831	N	N	N	N
vg0433246740	A -> T	LOC_Os04g55830.1	upstream_gene_variant ; 4264.0bp to feature; MODIFIER	silent_mutation	Average:29.889; most accessible tissue: Minghui63 root, score: 60.831	N	N	N	N
vg0433246740	A -> T	LOC_Os04g55840.1	intron_variant ; MODIFIER	silent_mutation	Average:29.889; most accessible tissue: Minghui63 root, score: 60.831	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0433246740	NA	6.70E-06	mr1054	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
vg0433246740	NA	8.35E-07	mr1057	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
vg0433246740	2.07E-06	2.07E-06	mr1214	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
vg0433246740	NA	8.22E-07	mr1345	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