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Detailed information for vg0502210759:

Variant ID: vg0502210759 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 2210759
Reference Allele: C	Alternative Allele: G
Primary Allele: C	Secondary Allele: G

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.64, G: 0.36, others allele: 0.00, population size: 111. )

Flanking Sequence (100 bp) in Reference Genome:

AAATTAAAGTAGAATAAGTAATATGGTACGTTGGCTAGTACAATAATGTAAGTAGGCTTAAACCCGCCATATATATTATCTAAGATATAATTGATGAATT[C/G]
TACCTCCGTTCTATATTGCACTTTATATCGGGAAAAGTGCATCTAGTTTCACTTTACATCAGGTTTAGCTCATAGTTTTAGTTTGCACCGGGTCGCTTTC

Reverse complement sequence

GAAAGCGACCCGGTGCAAACTAAAACTATGAGCTAAACCTGATGTAAAGTGAAACTAGATGCACTTTTCCCGATATAAAGTGCAATATAGAACGGAGGTA[G/C]
AATTCATCAATTATATCTTAGATAATATATATGGCGGGTTTAAGCCTACTTACATTATTGTACTAGCCAACGTACCATATTACTTATTCTACTTTAATTT

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	83.30%	12.70%	1.38%	2.54%	NA
All Indica	2759	75.80%	18.40%	2.28%	3.48%	NA
All Japonica	1512	98.00%	0.30%	0.07%	1.59%	NA
Aus	269	97.80%	1.90%	0.37%	0.00%	NA
Indica I	595	99.70%	0.00%	0.17%	0.17%	NA
Indica II	465	90.50%	8.80%	0.22%	0.43%	NA
Indica III	913	50.30%	41.40%	4.60%	3.72%	NA
Indica Intermediate	786	78.80%	11.30%	2.42%	7.51%	NA
Temperate Japonica	767	99.90%	0.10%	0.00%	0.00%	NA
Tropical Japonica	504	98.00%	0.20%	0.20%	1.59%	NA
Japonica Intermediate	241	92.10%	1.20%	0.00%	6.64%	NA
VI/Aromatic	96	20.80%	79.20%	0.00%	0.00%	NA
Intermediate	90	91.10%	8.90%	0.00%	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
vg0502210759	C -> DEL	N	N	silent_mutation	Average:38.865; most accessible tissue: Callus, score: 66.22	N	N	N	N
vg0502210759	C -> G	LOC_Os05g04680.1	upstream_gene_variant ; 2132.0bp to feature; MODIFIER	silent_mutation	Average:38.865; most accessible tissue: Callus, score: 66.22	N	N	N	N
vg0502210759	C -> G	LOC_Os05g04670.1	downstream_gene_variant ; 1991.0bp to feature; MODIFIER	silent_mutation	Average:38.865; most accessible tissue: Callus, score: 66.22	N	N	N	N
vg0502210759	C -> G	LOC_Os05g04670-LOC_Os05g04680	intergenic_region ; MODIFIER	silent_mutation	Average:38.865; most accessible tissue: Callus, score: 66.22	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0502210759	4.43E-07	1.41E-09	mr1794	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
vg0502210759	2.53E-06	1.08E-08	mr1794	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