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Detailed information for vg0600431653:

Variant ID: vg0600431653 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 431653
Reference Allele: G	Alternative Allele: T
Primary Allele: G	Secondary Allele: T

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.96, T: 0.03, others allele: 0.00, population size: 103. )

Flanking Sequence (100 bp) in Reference Genome:

GAAGAAATAAAGAAAGCAATTAATGTCAGAATTACCGGACTATCTGAACAGATTATTGGGCTTTCAACAGCAGCAACAAAAGTTTGAGACAACTTTCTTG[G/T]
AGTGATCTGCAAGATTTGTATAAATCAATATAATGTTCTAAAAAAGTATTCCTTATGAAGTTTGAAGTTATTAGACAAGTACCTTATTTATTAAAACAGG

Reverse complement sequence

CCTGTTTTAATAAATAAGGTACTTGTCTAATAACTTCAAACTTCATAAGGAATACTTTTTTAGAACATTATATTGATTTATACAAATCTTGCAGATCACT[C/A]
CAAGAAAGTTGTCTCAAACTTTTGTTGCTGCTGTTGAAAGCCCAATAATCTGTTCAGATAGTCCGGTAATTCTGACATTAATTGCTTTCTTTATTTCTTC

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	81.90%	14.00%	0.11%	3.96%	NA
All Indica	2759	70.60%	22.60%	0.18%	6.60%	NA
All Japonica	1512	98.10%	1.80%	0.00%	0.13%	NA
Aus	269	98.90%	1.10%	0.00%	0.00%	NA
Indica I	595	60.20%	37.60%	0.34%	1.85%	NA
Indica II	465	75.50%	6.00%	0.00%	18.49%	NA
Indica III	913	72.30%	25.30%	0.11%	2.30%	NA
Indica Intermediate	786	73.70%	17.90%	0.25%	8.14%	NA
Temperate Japonica	767	99.70%	0.00%	0.00%	0.26%	NA
Tropical Japonica	504	95.00%	5.00%	0.00%	0.00%	NA
Japonica Intermediate	241	99.20%	0.80%	0.00%	0.00%	NA
VI/Aromatic	96	99.00%	0.00%	0.00%	1.04%	NA
Intermediate	90	88.90%	8.90%	0.00%	2.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0600431653	G -> T	LOC_Os06g01730.1	downstream_gene_variant ; 1052.0bp to feature; MODIFIER	silent_mutation	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N
vg0600431653	G -> T	LOC_Os06g01740.1	intron_variant ; MODIFIER	silent_mutation	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N
vg0600431653	G -> DEL	N	N	silent_mutation	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0600431653	NA	2.00E-06	mr1627	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
vg0600431653	3.81E-07	NA	mr1728_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