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Detailed information for vg1220093634:

Variant ID: vg1220093634 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 20093634
Reference Allele: C	Alternative Allele: G
Primary Allele: C	Secondary Allele: G

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.67, G: 0.33, others allele: 0.00, population size: 93. )

Flanking Sequence (100 bp) in Reference Genome:

TAGGTTAACTGTTGTTTAATTTGCTCAAAGAACTGTAGAAAAATAAATACATTGCCAACCTTAGCTCGTCATGTTTGGAGAGGAACACTTGGAGACTTGG[C/G]
TGTTCAACAGAAAAGGGTTTAGAAGTTCATTATATATATATATATATGCTTCTTAATGATTTTCACTACTGCTATTTGGTAACCTTCGTATAAATCGTTC

Reverse complement sequence

GAACGATTTATACGAAGGTTACCAAATAGCAGTAGTGAAAATCATTAAGAAGCATATATATATATATATAATGAACTTCTAAACCCTTTTCTGTTGAACA[G/C]
CCAAGTCTCCAAGTGTTCCTCTCCAAACATGACGAGCTAAGGTTGGCAATGTATTTATTTTTCTACAGTTCTTTGAGCAAATTAAACAACAGTTAACCTA

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	43.70%	17.20%	7.72%	31.40%	NA
All Indica	2759	38.50%	12.50%	9.46%	39.51%	NA
All Japonica	1512	60.70%	13.60%	4.96%	20.70%	NA
Aus	269	14.50%	75.80%	5.20%	4.46%	NA
Indica I	595	38.70%	12.10%	17.65%	31.60%	NA
Indica II	465	57.20%	4.10%	8.39%	30.32%	NA
Indica III	913	24.50%	14.10%	2.85%	58.49%	NA
Indica Intermediate	786	43.50%	16.00%	11.58%	28.88%	NA
Temperate Japonica	767	88.90%	5.70%	1.69%	3.65%	NA
Tropical Japonica	504	22.60%	19.60%	9.92%	47.82%	NA
Japonica Intermediate	241	50.60%	26.10%	4.98%	18.26%	NA
VI/Aromatic	96	5.20%	36.50%	12.50%	45.83%	NA
Intermediate	90	46.70%	22.20%	3.33%	27.78%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1220093634	C -> DEL	N	N	silent_mutation	Average:40.639; most accessible tissue: Zhenshan97 young leaf, score: 57.78	N	N	N	N
vg1220093634	C -> G	LOC_Os12g33220.1	upstream_gene_variant ; 180.0bp to feature; MODIFIER	silent_mutation	Average:40.639; most accessible tissue: Zhenshan97 young leaf, score: 57.78	N	N	N	N
vg1220093634	C -> G	LOC_Os12g33210-LOC_Os12g33220	intergenic_region ; MODIFIER	silent_mutation	Average:40.639; most accessible tissue: Zhenshan97 young leaf, score: 57.78	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1220093634	4.57E-09	NA	mr1334	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
vg1220093634	1.42E-13	3.22E-26	mr1334	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
vg1220093634	NA	1.82E-09	mr1089_2	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
vg1220093634	NA	9.85E-07	mr1121_2	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
vg1220093634	2.57E-14	NA	mr1334_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
vg1220093634	8.39E-15	3.71E-31	mr1334_2	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
vg1220093634	1.23E-08	2.05E-14	mr1991_2	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