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Detailed information for vg0408191145:

Variant ID: vg0408191145 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 8191145
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AGACTTCAACCACCAAAAAGTGGCTAAGGTTGAGTTGTACATTCCAAATATCCAAGGGGCCCTTTTTTGGCTACAATAAGGGGGATTAGCGGCAGCCTGC[C/T]
GAATATACATCGTTCGCCTCTCCAGGCAAACACAAAAAGAAGGAAAACTACAAAAATCTAAGGAAAGGGCGGAGGGCCTCACACCTCTGGGTGATCCTGG

Reverse complement sequence

CCAGGATCACCCAGAGGTGTGAGGCCCTCCGCCCTTTCCTTAGATTTTTGTAGTTTTCCTTCTTTTTGTGTTTGCCTGGAGAGGCGAACGATGTATATTC[G/A]
GCAGGCTGCCGCTAATCCCCCTTATTGTAGCCAAAAAAGGGCCCCTTGGATATTTGGAATGTACAACTCAACCTTAGCCACTTTTTGGTGGTTGAAGTCT

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	60.30%	36.60%	1.14%	1.97%	NA
All Indica	2759	36.90%	59.20%	1.70%	2.28%	NA
All Japonica	1512	97.50%	0.40%	0.20%	1.92%	NA
Aus	269	77.00%	23.00%	0.00%	0.00%	NA
Indica I	595	41.50%	53.90%	1.51%	3.03%	NA
Indica II	465	36.80%	60.20%	1.51%	1.51%	NA
Indica III	913	31.00%	67.10%	0.77%	1.10%	NA
Indica Intermediate	786	40.20%	53.20%	3.05%	3.56%	NA
Temperate Japonica	767	99.00%	0.30%	0.00%	0.78%	NA
Tropical Japonica	504	98.80%	0.40%	0.00%	0.79%	NA
Japonica Intermediate	241	90.00%	0.80%	1.24%	7.88%	NA
VI/Aromatic	96	95.80%	4.20%	0.00%	0.00%	NA
Intermediate	90	67.80%	26.70%	4.44%	1.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0408191145	C -> DEL	N	N	silent_mutation	Average:49.473; most accessible tissue: Zhenshan97 flag leaf, score: 75.761	N	N	N	N
vg0408191145	C -> T	LOC_Os04g14590.1	downstream_gene_variant ; 1443.0bp to feature; MODIFIER	silent_mutation	Average:49.473; most accessible tissue: Zhenshan97 flag leaf, score: 75.761	N	N	N	N
vg0408191145	C -> T	LOC_Os04g14600.1	downstream_gene_variant ; 79.0bp to feature; MODIFIER	silent_mutation	Average:49.473; most accessible tissue: Zhenshan97 flag leaf, score: 75.761	N	N	N	N
vg0408191145	C -> T	LOC_Os04g14590-LOC_Os04g14600	intergenic_region ; MODIFIER	silent_mutation	Average:49.473; most accessible tissue: Zhenshan97 flag leaf, score: 75.761	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0408191145	1.72E-06	NA	mr1707	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
vg0408191145	NA	5.23E-06	mr1707	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