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Detailed information for vg0513325546:

Variant ID: vg0513325546 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 13325546
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, others allele: 0.00, population size: 241. )

Flanking Sequence (100 bp) in Reference Genome:

ATTTACCTGTGTTTTCCTGATGAAAGCAAAAATGTGGTCCACTGTTTCACGTGTACTACCTGCTGTTGAGAAATACGCCTATAGACTCCTTGATTTTCAA[C/T]
AACCCATTTTGGCTGCCAATTAGGCTATACAACTCCCTTAGATGAAAACATGGTTAATTTAATTGCCATCGACGGTGAGATTCAAGCCCATATCAAGTTG

Reverse complement sequence

CAACTTGATATGGGCTTGAATCTCACCGTCGATGGCAATTAAATTAACCATGTTTTCATCTAAGGGAGTTGTATAGCCTAATTGGCAGCCAAAATGGGTT[G/A]
TTGAAAATCAAGGAGTCTATAGGCGTATTTCTCAACAGCAGGTAGTACACGTGAAACAGTGGACCACATTTTTGCTTTCATCAGGAAAACACAGGTAAAT

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	76.20%	21.50%	2.29%	0.00%	NA
All Indica	2759	62.20%	34.20%	3.62%	0.00%	NA
All Japonica	1512	99.50%	0.50%	0.07%	0.00%	NA
Aus	269	80.30%	18.20%	1.49%	0.00%	NA
Indica I	595	76.80%	19.30%	3.87%	0.00%	NA
Indica II	465	65.80%	29.70%	4.52%	0.00%	NA
Indica III	913	55.30%	42.70%	1.97%	0.00%	NA
Indica Intermediate	786	57.00%	38.20%	4.83%	0.00%	NA
Temperate Japonica	767	99.60%	0.40%	0.00%	0.00%	NA
Tropical Japonica	504	99.40%	0.40%	0.20%	0.00%	NA
Japonica Intermediate	241	99.20%	0.80%	0.00%	0.00%	NA
VI/Aromatic	96	97.90%	2.10%	0.00%	0.00%	NA
Intermediate	90	81.10%	15.60%	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
vg0513325546	C -> T	LOC_Os05g23340.1	upstream_gene_variant ; 2104.0bp to feature; MODIFIER	silent_mutation	Average:49.114; most accessible tissue: Callus, score: 79.441	N	N	N	N
vg0513325546	C -> T	LOC_Os05g23350.1	downstream_gene_variant ; 2452.0bp to feature; MODIFIER	silent_mutation	Average:49.114; most accessible tissue: Callus, score: 79.441	N	N	N	N
vg0513325546	C -> T	LOC_Os05g23340-LOC_Os05g23350	intergenic_region ; MODIFIER	silent_mutation	Average:49.114; most accessible tissue: Callus, score: 79.441	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0513325546	NA	2.74E-08	mr1532	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
vg0513325546	NA	2.96E-06	mr1532	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
vg0513325546	9.06E-07	NA	mr1138_2	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
vg0513325546	7.43E-06	NA	mr1138_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
vg0513325546	NA	1.73E-06	mr1345_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
vg0513325546	NA	1.76E-06	mr1800_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