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Detailed information for vg1115030431:

Variant ID: vg1115030431 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 15030431
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, T: 0.01, others allele: 0.00, population size: 99. )

Flanking Sequence (100 bp) in Reference Genome:

ACGTTTCCTTTAATTAATTAGGTCCTTGTATATAAGTACACCATATATAATATATACTTCCTTTTATCGTTGTAGAATGGAGATTCAAAGGGCCCGACGG[C/T]
GGGGGGTTTTCGATACTGGATTCATCGACCCTCGGAAAGTAAATATGCACACATATATATAGTACACACATATATAAATGTGCACTTAATTAAGTAAATA

Reverse complement sequence

TATTTACTTAATTAAGTGCACATTTATATATGTGTGTACTATATATATGTGTGCATATTTACTTTCCGAGGGTCGATGAATCCAGTATCGAAAACCCCCC[G/A]
CCGTCGGGCCCTTTGAATCTCCATTCTACAACGATAAAAGGAAGTATATATTATATATGGTGTACTTATATACAAGGACCTAATTAATTAAAGGAAACGT

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	75.40%	16.80%	2.03%	5.73%	NA
All Indica	2759	58.90%	28.20%	3.30%	9.60%	NA
All Japonica	1512	99.20%	0.50%	0.07%	0.26%	NA
Aus	269	99.30%	0.70%	0.00%	0.00%	NA
Indica I	595	41.00%	35.30%	5.04%	18.66%	NA
Indica II	465	63.70%	20.60%	4.09%	11.61%	NA
Indica III	913	67.00%	29.50%	0.77%	2.74%	NA
Indica Intermediate	786	60.10%	26.00%	4.45%	9.54%	NA
Temperate Japonica	767	99.60%	0.10%	0.00%	0.26%	NA
Tropical Japonica	504	98.60%	1.00%	0.00%	0.40%	NA
Japonica Intermediate	241	99.20%	0.40%	0.41%	0.00%	NA
VI/Aromatic	96	95.80%	0.00%	4.17%	0.00%	NA
Intermediate	90	90.00%	7.80%	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
vg1115030431	C -> T	LOC_Os11g26240.1	downstream_gene_variant ; 2201.0bp to feature; MODIFIER	silent_mutation	Average:24.758; most accessible tissue: Minghui63 young leaf, score: 42.042	N	N	N	N
vg1115030431	C -> T	LOC_Os11g26250.1	downstream_gene_variant ; 333.0bp to feature; MODIFIER	silent_mutation	Average:24.758; most accessible tissue: Minghui63 young leaf, score: 42.042	N	N	N	N
vg1115030431	C -> T	LOC_Os11g26250-LOC_Os11g26270	intergenic_region ; MODIFIER	silent_mutation	Average:24.758; most accessible tissue: Minghui63 young leaf, score: 42.042	N	N	N	N
vg1115030431	C -> DEL	N	N	silent_mutation	Average:24.758; most accessible tissue: Minghui63 young leaf, score: 42.042	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1115030431	5.61E-06	5.61E-06	mr1289_2	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
vg1115030431	2.32E-06	1.83E-06	mr1824_2	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