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Detailed information for vg0515200395:

Variant ID: vg0515200395 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 15200395
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.01, others allele: 0.00, population size: 213. )

Flanking Sequence (100 bp) in Reference Genome:

CATTTGATCAATGACAGCGCAAATTATTCTGATTAAGTTTGTGTATATTATTGATCATGAGAAGTACGTGAAAATTTTCAATTCCCGGGAAGCATAGGCC[C/T]
AGGAGGAATCAAGTGGGAGTTCAGGGACATGCAACTGAGAATCTGCTGAGGTTTTCTCTGACATGATACGGTAAGATTGCCTTTCTTTGATGTTCTGATG

Reverse complement sequence

CATCAGAACATCAAAGAAAGGCAATCTTACCGTATCATGTCAGAGAAAACCTCAGCAGATTCTCAGTTGCATGTCCCTGAACTCCCACTTGATTCCTCCT[G/A]
GGCCTATGCTTCCCGGGAATTGAAAATTTTCACGTACTTCTCATGATCAATAATATACACAAACTTAATCAGAATAATTTGCGCTGTCATTGATCAAATG

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	66.20%	21.10%	2.54%	10.14%	NA
All Indica	2759	52.30%	29.40%	3.95%	14.35%	NA
All Japonica	1512	97.40%	0.90%	0.33%	1.32%	NA
Aus	269	27.10%	61.00%	0.74%	11.15%	NA
Indica I	595	64.40%	24.40%	7.23%	4.03%	NA
Indica II	465	64.30%	22.20%	2.80%	10.75%	NA
Indica III	913	45.50%	27.60%	2.41%	24.53%	NA
Indica Intermediate	786	44.10%	39.40%	3.94%	12.47%	NA
Temperate Japonica	767	97.40%	0.00%	0.39%	2.22%	NA
Tropical Japonica	504	97.60%	2.20%	0.20%	0.00%	NA
Japonica Intermediate	241	97.10%	1.20%	0.41%	1.24%	NA
VI/Aromatic	96	69.80%	1.00%	1.04%	28.12%	NA
Intermediate	90	80.00%	10.00%	3.33%	6.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0515200395	C -> T	LOC_Os05g26130.1	upstream_gene_variant ; 3004.0bp to feature; MODIFIER	silent_mutation	Average:37.047; most accessible tissue: Callus, score: 51.221	N	N	N	N
vg0515200395	C -> T	LOC_Os05g26130-LOC_Os05g26140	intergenic_region ; MODIFIER	silent_mutation	Average:37.047; most accessible tissue: Callus, score: 51.221	N	N	N	N
vg0515200395	C -> DEL	N	N	silent_mutation	Average:37.047; most accessible tissue: Callus, score: 51.221	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0515200395	NA	9.62E-06	mr1687	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
vg0515200395	NA	9.26E-07	mr1831	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