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Detailed information for vg0422210905:

Variant ID: vg0422210905 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 22210905
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.97, T: 0.04, others allele: 0.00, population size: 109. )

Flanking Sequence (100 bp) in Reference Genome:

AAACCAAACTCTGGCTAGGAATCTGGACACATGTGTGTCCAGGTTCGTAGCTAGGATTGGACTTTTTTTTGGGACGGAGGAGGTACACAATAATTGAGAG[C/T]
CCCATTGATTGCCCTAATAAACCAAAACCAAAAGTAAAATTTAAATTTTTAAACTTAATTTTGAAGTTGATTTTAAGATTTTTTTTTTAATGTAATTTTT

Reverse complement sequence

AAAAATTACATTAAAAAAAAAATCTTAAAATCAACTTCAAAATTAAGTTTAAAAATTTAAATTTTACTTTTGGTTTTGGTTTATTAGGGCAATCAATGGG[G/A]
CTCTCAATTATTGTGTACCTCCTCCGTCCCAAAAAAAAGTCCAATCCTAGCTACGAACCTGGACACACATGTGTCCAGATTCCTAGCCAGAGTTTGGTTT

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	57.90%	41.50%	0.47%	0.08%	NA
All Indica	2759	31.80%	67.50%	0.65%	0.11%	NA
All Japonica	1512	99.60%	0.30%	0.07%	0.07%	NA
Aus	269	71.00%	29.00%	0.00%	0.00%	NA
Indica I	595	12.30%	87.40%	0.34%	0.00%	NA
Indica II	465	13.30%	86.50%	0.22%	0.00%	NA
Indica III	913	50.60%	48.50%	0.77%	0.11%	NA
Indica Intermediate	786	35.60%	63.10%	1.02%	0.25%	NA
Temperate Japonica	767	99.60%	0.40%	0.00%	0.00%	NA
Tropical Japonica	504	99.60%	0.20%	0.00%	0.20%	NA
Japonica Intermediate	241	99.60%	0.00%	0.41%	0.00%	NA
VI/Aromatic	96	97.90%	2.10%	0.00%	0.00%	NA
Intermediate	90	76.70%	20.00%	3.33%	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
vg0422210905	C -> DEL	N	N	silent_mutation	Average:36.311; most accessible tissue: Zhenshan97 panicle, score: 49.416	N	N	N	N
vg0422210905	C -> T	LOC_Os04g36790.1	upstream_gene_variant ; 1674.0bp to feature; MODIFIER	silent_mutation	Average:36.311; most accessible tissue: Zhenshan97 panicle, score: 49.416	N	N	N	N
vg0422210905	C -> T	LOC_Os04g36770.1	downstream_gene_variant ; 4980.0bp to feature; MODIFIER	silent_mutation	Average:36.311; most accessible tissue: Zhenshan97 panicle, score: 49.416	N	N	N	N
vg0422210905	C -> T	LOC_Os04g36780.1	downstream_gene_variant ; 1409.0bp to feature; MODIFIER	silent_mutation	Average:36.311; most accessible tissue: Zhenshan97 panicle, score: 49.416	N	N	N	N
vg0422210905	C -> T	LOC_Os04g36780-LOC_Os04g36790	intergenic_region ; MODIFIER	silent_mutation	Average:36.311; most accessible tissue: Zhenshan97 panicle, score: 49.416	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0422210905	NA	3.53E-07	mr1177	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
vg0422210905	NA	8.51E-10	mr1352	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
vg0422210905	NA	5.30E-09	mr1929	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
vg0422210905	NA	1.22E-08	mr1172_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
vg0422210905	NA	2.05E-08	mr1212_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
vg0422210905	NA	4.31E-07	mr1559_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