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Detailed information for vg0609451875:

Variant ID: vg0609451875 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 9451875
Reference Allele: T	Alternative Allele: A
Primary Allele: A	Secondary Allele: T

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.89, A: 0.11, others allele: 0.00, population size: 70. )

Flanking Sequence (100 bp) in Reference Genome:

TACTTTTTTGGATCGGACTTATTTTTTTTCTTTTTTTGCCGGTTTTTCCCCCTCTTTCGCCCTTTTTGATCTGACATGTTTTGTTTTTTTTTTCACACGG[T/A]
TTTTTTTCGCGTGTGGATTTTTTTTCGTTTGTTTCGTCTATTTTTTTATCGGACATAGTTTTTTGTTCGTCTGGTTTTTTTCGCATGGTTTTTTTCTCTC

Reverse complement sequence

GAGAGAAAAAAACCATGCGAAAAAAACCAGACGAACAAAAAACTATGTCCGATAAAAAAATAGACGAAACAAACGAAAAAAAATCCACACGCGAAAAAAA[A/T]
CCGTGTGAAAAAAAAAACAAAACATGTCAGATCAAAAAGGGCGAAAGAGGGGGAAAAACCGGCAAAAAAAGAAAAAAAATAAGTCCGATCCAAAAAAGTA

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	44.70%	12.20%	0.08%	43.04%	NA
All Indica	2759	73.80%	4.10%	0.04%	22.00%	NA
All Japonica	1512	2.10%	29.60%	0.07%	68.25%	NA
Aus	269	1.90%	1.10%	0.00%	97.03%	NA
Indica I	595	82.50%	1.50%	0.00%	15.97%	NA
Indica II	465	82.40%	0.60%	0.00%	16.99%	NA
Indica III	913	61.10%	10.20%	0.11%	28.59%	NA
Indica Intermediate	786	77.00%	1.10%	0.00%	21.88%	NA
Temperate Japonica	767	1.80%	54.60%	0.00%	43.55%	NA
Tropical Japonica	504	2.00%	1.20%	0.20%	96.63%	NA
Japonica Intermediate	241	3.30%	9.10%	0.00%	87.55%	NA
VI/Aromatic	96	4.20%	2.10%	0.00%	93.75%	NA
Intermediate	90	38.90%	10.00%	2.22%	48.89%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0609451875	T -> A	LOC_Os06g16460-LOC_Os06g16470	intergenic_region ; MODIFIER	silent_mutation	Average:26.907; most accessible tissue: Minghui63 panicle, score: 42.799	N	N	N	N
vg0609451875	T -> DEL	N	N	silent_mutation	Average:26.907; most accessible tissue: Minghui63 panicle, score: 42.799	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0609451875	NA	3.67E-06	mr1096	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
vg0609451875	NA	6.16E-08	mr1090_2	Jap_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
vg0609451875	NA	3.70E-06	mr1094_2	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
vg0609451875	NA	3.04E-06	mr1096_2	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
vg0609451875	NA	9.76E-07	mr1211_2	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
vg0609451875	NA	4.85E-10	mr1570_2	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