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Detailed information for vg0401672905:

Variant ID: vg0401672905 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 1672905
Reference Allele: T	Alternative Allele: A
Primary Allele: T	Secondary Allele: A

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.91, A: 0.10, others allele: 0.00, population size: 94. )

Flanking Sequence (100 bp) in Reference Genome:

GGAAAAACCATCACCTCTAAACCCCTCATAGGTAATCCTTGCTTTTTAATTTACCCCTAAACACTTCCTATTATACTTGATATTCTTTTAACTTTTTCCT[T/A]
CAGATTTAATTGGGGTAGTCAGTCGTATTGGTCCATATGATTTCGCGAGCCCAACATCAGACAAAAAACTCAGAAGAATTCAAATTCAGAACCAAGAGTA

Reverse complement sequence

TACTCTTGGTTCTGAATTTGAATTCTTCTGAGTTTTTTGTCTGATGTTGGGCTCGCGAAATCATATGGACCAATACGACTGACTACCCCAATTAAATCTG[A/T]
AGGAAAAAGTTAAAAGAATATCAAGTATAATAGGAAGTGTTTAGGGGTAAATTAAAAAGCAAGGATTACCTATGAGGGGTTTAGAGGTGATGGTTTTTCC

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	23.80%	11.60%	0.40%	64.13%	NA
All Indica	2759	10.90%	16.60%	0.58%	71.91%	NA
All Japonica	1512	51.60%	1.90%	0.13%	46.36%	NA
Aus	269	8.20%	4.50%	0.37%	86.99%	NA
Indica I	595	24.70%	5.40%	1.18%	68.74%	NA
Indica II	465	8.20%	40.40%	0.22%	51.18%	NA
Indica III	913	1.90%	6.90%	0.22%	91.02%	NA
Indica Intermediate	786	12.50%	22.40%	0.76%	64.38%	NA
Temperate Japonica	767	82.40%	0.50%	0.13%	16.95%	NA
Tropical Japonica	504	16.90%	3.40%	0.20%	79.56%	NA
Japonica Intermediate	241	26.10%	3.30%	0.00%	70.54%	NA
VI/Aromatic	96	2.10%	33.30%	0.00%	64.58%	NA
Intermediate	90	25.60%	18.90%	0.00%	55.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0401672905	T -> DEL	N	N	silent_mutation	Average:6.0; most accessible tissue: Callus, score: 21.328	N	N	N	N
vg0401672905	T -> A	LOC_Os04g03760.1	downstream_gene_variant ; 3704.0bp to feature; MODIFIER	silent_mutation	Average:6.0; most accessible tissue: Callus, score: 21.328	N	N	N	N
vg0401672905	T -> A	LOC_Os04g03740-LOC_Os04g03760	intergenic_region ; MODIFIER	silent_mutation	Average:6.0; most accessible tissue: Callus, score: 21.328	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0401672905	NA	1.57E-11	mr1829	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
vg0401672905	9.13E-07	NA	mr1842	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
vg0401672905	NA	3.58E-07	mr1842	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
vg0401672905	NA	4.13E-07	mr1062_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
vg0401672905	NA	4.65E-09	mr1829_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