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Detailed information for vg0405892464:

Variant ID: vg0405892464 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 5892464
Reference Allele: T	Alternative Allele: A
Primary Allele: T	Secondary Allele: A

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.94, A: 0.06, others allele: 0.00, population size: 78. )

Flanking Sequence (100 bp) in Reference Genome:

CGTTGTTGTGTCGTGGATAGGTGGACAATGGGAGCAAAGGCGGCATTTAGGTCAGACAGGAATACCGATCCTAATGTGTGGTCTAAACACATGGTTCGTT[T/A]
TCGTAGCCTCCGAAATCTGGGTAGTGATGCTTTCTTTGAGGCCGCTAGGAACCCTGAGCAGACAGAAAAGGCGATGGATTTCTTAAAGGGGATTTTGGAT

Reverse complement sequence

ATCCAAAATCCCCTTTAAGAAATCCATCGCCTTTTCTGTCTGCTCAGGGTTCCTAGCGGCCTCAAAGAAAGCATCACTACCCAGATTTCGGAGGCTACGA[A/T]
AACGAACCATGTGTTTAGACCACACATTAGGATCGGTATTCCTGTCTGACCTAAATGCCGCCTTTGCTCCCATTGTCCACCTATCCACGACACAACAACG

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	26.80%	2.90%	1.86%	68.39%	NA
All Indica	2759	8.60%	3.70%	2.50%	85.21%	NA
All Japonica	1512	64.20%	0.10%	0.33%	35.45%	NA
Aus	269	9.30%	11.90%	3.35%	75.46%	NA
Indica I	595	2.40%	9.90%	6.39%	81.34%	NA
Indica II	465	14.20%	0.90%	1.08%	83.87%	NA
Indica III	913	11.00%	0.40%	1.20%	87.40%	NA
Indica Intermediate	786	7.40%	4.30%	1.91%	86.39%	NA
Temperate Japonica	767	69.50%	0.10%	0.13%	30.25%	NA
Tropical Japonica	504	48.40%	0.00%	0.60%	50.99%	NA
Japonica Intermediate	241	80.10%	0.00%	0.41%	19.50%	NA
VI/Aromatic	96	7.30%	2.10%	5.21%	85.42%	NA
Intermediate	90	31.10%	2.20%	0.00%	66.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0405892464	T -> DEL	LOC_Os04g10860.1	N	frameshift_variant	Average:9.143; most accessible tissue: Callus, score: 23.501	N	N	N	N
vg0405892464	T -> A	LOC_Os04g10860.1	missense_variant ; p.Phe447Tyr; MODERATE	nonsynonymous_codon ; F447Y	Average:9.143; most accessible tissue: Callus, score: 23.501	benign	-0.037	TOLERATED	1.00

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0405892464	NA	7.13E-08	mr1190	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
vg0405892464	1.24E-06	1.04E-10	mr1227	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
vg0405892464	NA	4.95E-06	mr1227	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
vg0405892464	NA	4.65E-07	mr1245	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
vg0405892464	NA	4.27E-09	mr1275	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
vg0405892464	NA	2.13E-14	mr1361	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
vg0405892464	NA	5.68E-06	mr1373	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
vg0405892464	NA	9.96E-07	mr1450	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
vg0405892464	NA	3.21E-06	mr1574	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
vg0405892464	NA	9.00E-08	mr1622	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
vg0405892464	NA	7.51E-08	mr1677	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
vg0405892464	NA	8.45E-14	mr1726	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
vg0405892464	NA	1.99E-09	mr1866	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