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Detailed information for vg0402509050:

Variant ID: vg0402509050 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 2509050
Reference Allele: C	Alternative Allele: T
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 108. )

Flanking Sequence (100 bp) in Reference Genome:

GTACCTCCACTAACATTATAATCACCAAAATGCATAAACCATCTTCCTCAGATCATTTACCATGTGTTTGTTGGATTATCTTGATGATTCAGACTGCAAT[C/T]
AAGCTAAAAAATGCAAGCATCTTTACTGTGTTTCTCAAAAAAAAAAAATGCAAGCATATTCCACTCCTATACTAGGTGCAATAGCTAGCCAGCTTTAATA

Reverse complement sequence

TATTAAAGCTGGCTAGCTATTGCACCTAGTATAGGAGTGGAATATGCTTGCATTTTTTTTTTTTGAGAAACACAGTAAAGATGCTTGCATTTTTTAGCTT[G/A]
ATTGCAGTCTGAATCATCAAGATAATCCAACAAACACATGGTAAATGATCTGAGGAAGATGGTTTATGCATTTTGGTGATTATAATGTTAGTGGAGGTAC

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	71.70%	28.00%	0.28%	0.00%	NA
All Indica	2759	80.50%	19.10%	0.33%	0.00%	NA
All Japonica	1512	52.60%	47.20%	0.20%	0.00%	NA
Aus	269	88.80%	11.20%	0.00%	0.00%	NA
Indica I	595	91.60%	8.40%	0.00%	0.00%	NA
Indica II	465	68.60%	30.80%	0.65%	0.00%	NA
Indica III	913	86.30%	13.60%	0.11%	0.00%	NA
Indica Intermediate	786	72.50%	26.80%	0.64%	0.00%	NA
Temperate Japonica	767	24.40%	75.50%	0.13%	0.00%	NA
Tropical Japonica	504	82.30%	17.50%	0.20%	0.00%	NA
Japonica Intermediate	241	80.50%	19.10%	0.41%	0.00%	NA
VI/Aromatic	96	71.90%	28.10%	0.00%	0.00%	NA
Intermediate	90	71.10%	27.80%	1.11%	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
vg0402509050	C -> T	LOC_Os04g05080.1	upstream_gene_variant ; 2433.0bp to feature; MODIFIER	silent_mutation	Average:51.117; most accessible tissue: Callus, score: 81.742	N	N	N	N
vg0402509050	C -> T	LOC_Os04g05070-LOC_Os04g05080	intergenic_region ; MODIFIER	silent_mutation	Average:51.117; most accessible tissue: Callus, score: 81.742	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0402509050	NA	8.73E-07	mr1668	Jap_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
vg0402509050	NA	6.00E-07	mr1277_2	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