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Detailed information for vg1218085065:

Variant ID: vg1218085065 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 18085065
Reference Allele: G	Alternative Allele: T
Primary Allele: T	Secondary Allele: G

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.83, G: 0.16, others allele: 0.00, population size: 99. )

Flanking Sequence (100 bp) in Reference Genome:

ACCTCCGGTACCAAACATGATAACCCATAGGTATTATCAGCCTCATTGGATGGCATATTATATGAATATGCCAAATGGCATACTTATAAACGAAAATCAA[G/T]
TTGTGAATAAAACTTTTATATATGTGTTTTTAGCGATCCAAAAGTAAAGGCTGAAAAATAAACTTCGATGAAAAAACCCCAAAATCAGCTCCAAATTTAA

Reverse complement sequence

TTAAATTTGGAGCTGATTTTGGGGTTTTTTCATCGAAGTTTATTTTTCAGCCTTTACTTTTGGATCGCTAAAAACACATATATAAAAGTTTTATTCACAA[C/A]
TTGATTTTCGTTTATAAGTATGCCATTTGGCATATTCATATAATATGCCATCCAATGAGGCTGATAATACCTATGGGTTATCATGTTTGGTACCGGAGGT

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	48.20%	47.60%	0.08%	4.15%	NA
All Indica	2759	46.40%	52.00%	0.00%	1.59%	NA
All Japonica	1512	54.70%	45.20%	0.00%	0.13%	NA
Aus	269	23.80%	30.10%	0.37%	45.72%	NA
Indica I	595	5.40%	94.50%	0.00%	0.17%	NA
Indica II	465	68.60%	30.30%	0.00%	1.08%	NA
Indica III	913	64.30%	33.40%	0.00%	2.30%	NA
Indica Intermediate	786	43.50%	54.30%	0.00%	2.16%	NA
Temperate Japonica	767	35.20%	64.80%	0.00%	0.00%	NA
Tropical Japonica	504	77.60%	22.40%	0.00%	0.00%	NA
Japonica Intermediate	241	68.90%	30.30%	0.00%	0.83%	NA
VI/Aromatic	96	72.90%	8.30%	0.00%	18.75%	NA
Intermediate	90	40.00%	46.70%	3.33%	10.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1218085065	G -> DEL	N	N	silent_mutation	Average:45.629; most accessible tissue: Callus, score: 70.699	N	N	N	N
vg1218085065	G -> T	LOC_Os12g30130-LOC_Os12g30140	intergenic_region ; MODIFIER	silent_mutation	Average:45.629; most accessible tissue: Callus, score: 70.699	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1218085065	NA	8.74E-06	mr1010	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
vg1218085065	NA	4.58E-06	mr1060	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
vg1218085065	NA	2.88E-08	mr1163	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
vg1218085065	NA	5.33E-06	mr1170	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
vg1218085065	NA	6.59E-06	mr1188	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
vg1218085065	NA	7.49E-07	mr1192	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
vg1218085065	NA	6.74E-06	mr1280	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
vg1218085065	NA	7.76E-06	mr1353	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
vg1218085065	NA	9.36E-06	mr1359	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
vg1218085065	NA	1.70E-07	mr1397	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
vg1218085065	NA	5.21E-09	mr1486	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
vg1218085065	NA	3.46E-06	mr1548	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
vg1218085065	NA	1.11E-07	mr1557	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
vg1218085065	NA	8.77E-09	mr1857	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
vg1218085065	NA	5.63E-06	mr1857	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
vg1218085065	NA	8.86E-06	mr1232_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
vg1218085065	NA	8.03E-09	mr1557_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
vg1218085065	NA	4.24E-09	mr1565_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
vg1218085065	NA	1.22E-09	mr1598_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