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Detailed information for vg1218628528:

Variant ID: vg1218628528 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 18628528
Reference Allele: C	Alternative Allele: G
Primary Allele: C	Secondary Allele: G

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 117. )

Flanking Sequence (100 bp) in Reference Genome:

TAGACATGTCTTCTCGATTTGGCCATACTAGGAGTATTCATCATCCAAAATTGTTCCTAATCCCTACCATGCCTAATAATATGTTGTATGGGATGGTTTC[C/G]
TAGAGTGCAACATAGAAAACCTTAAGGAAGGGATGCCAAAACTTAGTCATGTTCTCGATCTTTTGTTGCTCATTTGAACACACGGATTTCCTATACGAAT

Reverse complement sequence

ATTCGTATAGGAAATCCGTGTGTTCAAATGAGCAACAAAAGATCGAGAACATGACTAAGTTTTGGCATCCCTTCCTTAAGGTTTTCTATGTTGCACTCTA[G/C]
GAAACCATCCCATACAACATATTATTAGGCATGGTAGGGATTAGGAACAATTTTGGATGATGAATACTCCTAGTATGGCCAAATCGAGAAGACATGTCTA

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	60.70%	35.60%	2.09%	1.63%	NA
All Indica	2759	34.40%	59.50%	3.37%	2.75%	NA
All Japonica	1512	98.70%	0.90%	0.33%	0.07%	NA
Aus	269	98.90%	0.70%	0.37%	0.00%	NA
Indica I	595	55.30%	38.80%	5.88%	0.00%	NA
Indica II	465	12.30%	69.50%	5.38%	12.90%	NA
Indica III	913	31.80%	67.10%	0.66%	0.44%	NA
Indica Intermediate	786	34.60%	60.40%	3.44%	1.53%	NA
Temperate Japonica	767	98.70%	1.00%	0.26%	0.00%	NA
Tropical Japonica	504	99.40%	0.20%	0.40%	0.00%	NA
Japonica Intermediate	241	97.10%	2.10%	0.41%	0.41%	NA
VI/Aromatic	96	97.90%	2.10%	0.00%	0.00%	NA
Intermediate	90	75.60%	24.40%	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
vg1218628528	C -> DEL	N	N	silent_mutation	Average:36.801; most accessible tissue: Callus, score: 68.823	N	N	N	N
vg1218628528	C -> G	LOC_Os12g31020.1	downstream_gene_variant ; 3055.0bp to feature; MODIFIER	silent_mutation	Average:36.801; most accessible tissue: Callus, score: 68.823	N	N	N	N
vg1218628528	C -> G	LOC_Os12g31000-LOC_Os12g31020	intergenic_region ; MODIFIER	silent_mutation	Average:36.801; most accessible tissue: Callus, score: 68.823	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1218628528	NA	8.98E-08	mr1090	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
vg1218628528	NA	1.66E-07	mr1321	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
vg1218628528	6.50E-09	9.45E-20	mr1457	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
vg1218628528	3.83E-07	3.06E-11	mr1457	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
vg1218628528	7.68E-15	9.52E-58	mr1458	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
vg1218628528	6.64E-11	5.48E-18	mr1458	Ind_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
vg1218628528	NA	4.34E-06	mr1686	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
vg1218628528	NA	4.17E-07	mr1090_2	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
vg1218628528	1.88E-08	5.17E-27	mr1457_2	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
vg1218628528	1.91E-06	1.22E-11	mr1457_2	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
vg1218628528	8.11E-15	2.42E-60	mr1458_2	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
vg1218628528	3.22E-12	2.42E-20	mr1458_2	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
vg1218628528	NA	4.66E-07	mr1805_2	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