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Detailed information for vg0622353554:

Variant ID: vg0622353554 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 22353554
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.62, C: 0.37, others allele: 0.00, population size: 245. )

Flanking Sequence (100 bp) in Reference Genome:

GACAAATATTTTGTACCGGATTTCTTGGATAAGCTTAAGAGCGGTCAAAATGAATCGAAGTATTGGTACTTCTATGGTTTCTTGTCAGCAATATTTGTTG[T/C]
AGAGGTATTATTCATTATATTTGGATCACTTATTTTGCAAAGGGAGGACAAACAACTAAGAGAACTAGCTGAGGTTGGCTATGAAATGATAACCAACCAT

Reverse complement sequence

ATGGTTGGTTATCATTTCATAGCCAACCTCAGCTAGTTCTCTTAGTTGTTTGTCCTCCCTTTGCAAAATAAGTGATCCAAATATAATGAATAATACCTCT[A/G]
CAACAAATATTGCTGACAAGAAACCATAGAAGTACCAATACTTCGATTCATTTTGACCGCTCTTAAGCTTATCCAAGAAATCCGGTACAAAATATTTGTC

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	68.40%	31.30%	0.19%	0.11%	NA
All Indica	2759	68.50%	31.00%	0.29%	0.18%	NA
All Japonica	1512	66.10%	33.90%	0.07%	0.00%	NA
Aus	269	87.40%	12.60%	0.00%	0.00%	NA
Indica I	595	85.50%	14.10%	0.17%	0.17%	NA
Indica II	465	79.80%	19.80%	0.43%	0.00%	NA
Indica III	913	48.30%	51.40%	0.22%	0.11%	NA
Indica Intermediate	786	72.50%	26.70%	0.38%	0.38%	NA
Temperate Japonica	767	77.80%	22.20%	0.00%	0.00%	NA
Tropical Japonica	504	59.30%	40.50%	0.20%	0.00%	NA
Japonica Intermediate	241	42.70%	57.30%	0.00%	0.00%	NA
VI/Aromatic	96	52.10%	47.90%	0.00%	0.00%	NA
Intermediate	90	65.60%	34.40%	0.00%	0.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0622353554	T -> C	LOC_Os06g37750.1	missense_variant ; p.Val466Ala; MODERATE	nonsynonymous_codon ; V466A	Average:61.088; most accessible tissue: Callus, score: 89.898	unknown	unknown	TOLERATED	0.21
vg0622353554	T -> DEL	LOC_Os06g37750.1	N	frameshift_variant	Average:61.088; most accessible tissue: Callus, score: 89.898	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0622353554	NA	7.95E-08	mr1037	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
vg0622353554	2.22E-06	6.30E-09	mr1066	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
vg0622353554	2.06E-06	1.06E-06	mr1265	Ind_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
vg0622353554	4.76E-06	5.87E-07	mr1528	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
vg0622353554	NA	4.33E-06	mr1574	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