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Detailed information for vg1227342306:

Variant ID: vg1227342306 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 27342306
Reference Allele: G	Alternative Allele: A
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.62, A: 0.38, others allele: 0.00, population size: 286. )

Flanking Sequence (100 bp) in Reference Genome:

GGTTGACATTGAGCCAATCACAATGCCATTCAGGAAGTGCGATGTTTTGTTGTTGTTGATTGGTGAAACGCCTGTTTGCGACAGAGAGATGAAACCATCA[G/A]
TTAGTCACACACACATTGCACCAAATTTGGTGAGAAGAGCTTCAACACTGAGAAGATGGCTTAGAAATGGAAGACTTGCCAGCTGAGGAGAGGGGATCAG

Reverse complement sequence

CTGATCCCCTCTCCTCAGCTGGCAAGTCTTCCATTTCTAAGCCATCTTCTCAGTGTTGAAGCTCTTCTCACCAAATTTGGTGCAATGTGTGTGTGACTAA[C/T]
TGATGGTTTCATCTCTCTGTCGCAAACAGGCGTTTCACCAATCAACAACAACAAAACATCGCACTTCCTGAATGGCATTGTGATTGGCTCAATGTCAACC

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	59.90%	40.10%	0.00%	0.00%	NA
All Indica	2759	96.40%	3.60%	0.00%	0.00%	NA
All Japonica	1512	0.80%	99.20%	0.00%	0.00%	NA
Aus	269	36.80%	63.20%	0.00%	0.00%	NA
Indica I	595	98.80%	1.20%	0.00%	0.00%	NA
Indica II	465	97.40%	2.60%	0.00%	0.00%	NA
Indica III	913	95.80%	4.20%	0.00%	0.00%	NA
Indica Intermediate	786	94.50%	5.50%	0.00%	0.00%	NA
Temperate Japonica	767	0.50%	99.50%	0.00%	0.00%	NA
Tropical Japonica	504	0.80%	99.20%	0.00%	0.00%	NA
Japonica Intermediate	241	1.70%	98.30%	0.00%	0.00%	NA
VI/Aromatic	96	14.60%	85.40%	0.00%	0.00%	NA
Intermediate	90	51.10%	48.90%	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
vg1227342306	G -> A	LOC_Os12g44080.1	upstream_gene_variant ; 4526.0bp to feature; MODIFIER	silent_mutation	Average:58.907; most accessible tissue: Callus, score: 82.031	N	N	N	N
vg1227342306	G -> A	LOC_Os12g44100.1	downstream_gene_variant ; 3816.0bp to feature; MODIFIER	silent_mutation	Average:58.907; most accessible tissue: Callus, score: 82.031	N	N	N	N
vg1227342306	G -> A	LOC_Os12g44090.1	intron_variant ; MODIFIER	silent_mutation	Average:58.907; most accessible tissue: Callus, score: 82.031	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1227342306	NA	2.10E-20	mr1021	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
vg1227342306	NA	3.62E-24	mr1551	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
vg1227342306	NA	4.25E-42	mr1721	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
vg1227342306	NA	4.94E-28	mr1793	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
vg1227342306	NA	5.16E-17	mr1916	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
vg1227342306	NA	2.15E-21	mr1943	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
vg1227342306	NA	7.93E-26	mr1323_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
vg1227342306	NA	1.41E-13	mr1325_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
vg1227342306	NA	9.33E-14	mr1326_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
vg1227342306	NA	1.82E-21	mr1551_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
vg1227342306	NA	1.66E-76	mr1671_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
vg1227342306	NA	1.95E-49	mr1721_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
vg1227342306	NA	5.63E-16	mr1744_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
vg1227342306	NA	2.47E-26	mr1916_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