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Detailed information for vg0500894385:

Variant ID: vg0500894385 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 894385
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: 122. )

Flanking Sequence (100 bp) in Reference Genome:

AGTTAGAAGTTGGAAGTTTGGAAGTGTGGCCGTTCCAAACTGTTTCTTCAAACTTGCAACTTTTCCATCACATCAAAACTTTTCTACACACATAAACTTC[C/T]
AACTTTTCCGTCACATCATTCCAATTTCAACCAAACTTTCAATTTTGGCATGAACTAAACACAGCCTAAACTCGGCTGAAACCATACTTAGAATTGTAAT

Reverse complement sequence

ATTACAATTCTAAGTATGGTTTCAGCCGAGTTTAGGCTGTGTTTAGTTCATGCCAAAATTGAAAGTTTGGTTGAAATTGGAATGATGTGACGGAAAAGTT[G/A]
GAAGTTTATGTGTGTAGAAAAGTTTTGATGTGATGGAAAAGTTGCAAGTTTGAAGAAACAGTTTGGAACGGCCACACTTCCAAACTTCCAACTTCTAACT

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	76.90%	2.80%	0.30%	20.02%	NA
All Indica	2759	65.90%	0.20%	0.47%	33.49%	NA
All Japonica	1512	91.90%	8.00%	0.00%	0.07%	NA
Aus	269	99.30%	0.00%	0.00%	0.74%	NA
Indica I	595	79.30%	0.00%	0.34%	20.34%	NA
Indica II	465	70.50%	0.00%	0.86%	28.60%	NA
Indica III	913	47.30%	0.30%	0.22%	52.14%	NA
Indica Intermediate	786	74.40%	0.30%	0.64%	24.68%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	78.40%	21.40%	0.00%	0.20%	NA
Japonica Intermediate	241	94.60%	5.40%	0.00%	0.00%	NA
VI/Aromatic	96	87.50%	0.00%	0.00%	12.50%	NA
Intermediate	90	85.60%	5.60%	1.11%	7.78%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0500894385	C -> T	LOC_Os05g02564.1	upstream_gene_variant ; 894.0bp to feature; MODIFIER	silent_mutation	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N
vg0500894385	C -> T	LOC_Os05g02580.1	upstream_gene_variant ; 4470.0bp to feature; MODIFIER	silent_mutation	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N
vg0500894385	C -> T	LOC_Os05g02560.1	downstream_gene_variant ; 2878.0bp to feature; MODIFIER	silent_mutation	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N
vg0500894385	C -> T	LOC_Os05g02570.1	downstream_gene_variant ; 593.0bp to feature; MODIFIER	silent_mutation	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N
vg0500894385	C -> T	LOC_Os05g02564-LOC_Os05g02570	intergenic_region ; MODIFIER	silent_mutation	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N
vg0500894385	C -> 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
vg0500894385	3.22E-07	3.21E-07	mr1918	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