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Detailed information for vg0203898222:

Variant ID: vg0203898222 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 3898222
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.99, others allele: 0.00, population size: 227. )

Flanking Sequence (100 bp) in Reference Genome:

ACACACTTGACAGGCATCCGAATATAAAAACTCTAAAGATTACCCATCAAGTATTATGAAGATTATGGTAATAAATAAGTCGAATAGCCTAGGCCATGAC[T/C]
ATTTACCATAATGAAAATAGGTATATCACATACCAAGGAAGTGACTATAGTAAAAACAAGTCATTCCTAGTTAACCCAAACAGCTTTTGTAGCCTAAAAA

Reverse complement sequence

TTTTTAGGCTACAAAAGCTGTTTGGGTTAACTAGGAATGACTTGTTTTTACTATAGTCACTTCCTTGGTATGTGATATACCTATTTTCATTATGGTAAAT[A/G]
GTCATGGCCTAGGCTATTCGACTTATTTATTACCATAATCTTCATAATACTTGATGGGTAATCTTTAGAGTTTTTATATTCGGATGCCTGTCAAGTGTGT

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	35.80%	4.40%	21.52%	38.26%	NA
All Indica	2759	31.70%	0.20%	16.24%	51.87%	NA
All Japonica	1512	44.20%	12.70%	32.61%	10.45%	NA
Aus	269	11.50%	0.00%	17.10%	71.38%	NA
Indica I	595	21.20%	0.00%	11.09%	67.73%	NA
Indica II	465	17.20%	0.40%	18.49%	63.87%	NA
Indica III	913	45.00%	0.30%	19.06%	35.60%	NA
Indica Intermediate	786	32.70%	0.10%	15.52%	51.65%	NA
Temperate Japonica	767	71.30%	1.40%	15.91%	11.34%	NA
Tropical Japonica	504	6.90%	30.20%	54.56%	8.33%	NA
Japonica Intermediate	241	36.10%	12.00%	39.83%	12.03%	NA
VI/Aromatic	96	85.40%	0.00%	13.54%	1.04%	NA
Intermediate	90	41.10%	11.10%	18.89%	28.89%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0203898222	T -> DEL	N	N	silent_mutation	Average:8.906; most accessible tissue: Callus, score: 19.376	N	N	N	N
vg0203898222	T -> C	LOC_Os02g07520.1	upstream_gene_variant ; 2780.0bp to feature; MODIFIER	silent_mutation	Average:8.906; most accessible tissue: Callus, score: 19.376	N	N	N	N
vg0203898222	T -> C	LOC_Os02g07530.1	upstream_gene_variant ; 575.0bp to feature; MODIFIER	silent_mutation	Average:8.906; most accessible tissue: Callus, score: 19.376	N	N	N	N
vg0203898222	T -> C	LOC_Os02g07540.1	downstream_gene_variant ; 3836.0bp to feature; MODIFIER	silent_mutation	Average:8.906; most accessible tissue: Callus, score: 19.376	N	N	N	N
vg0203898222	T -> C	LOC_Os02g07520-LOC_Os02g07530	intergenic_region ; MODIFIER	silent_mutation	Average:8.906; most accessible tissue: Callus, score: 19.376	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0203898222	NA	1.66E-06	mr1518	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