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Detailed information for vg1218704534:

Variant ID: vg1218704534 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 18704534
Reference Allele: C	Alternative Allele: T
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.67, C: 0.32, others allele: 0.00, population size: 186. )

Flanking Sequence (100 bp) in Reference Genome:

TAATTTACATTTATATCCTTGCATAGGAAGAAATCGCAGAAATGTACATATGTCGCAGATTGAAAATGCGGGTGGGATCACAAATCGCGTTGTGGTGACG[C/T]
GGGACGACCAGACCGTTGTGGTGACTGCTGGATGGTGGCGGACATGGCAAAGAAGAGAAGCTTTCAGGAGGACCCTGGACACTGGTGTCTCTTACCTTTT

Reverse complement sequence

AAAAGGTAAGAGACACCAGTGTCCAGGGTCCTCCTGAAAGCTTCTCTTCTTTGCCATGTCCGCCACCATCCAGCAGTCACCACAACGGTCTGGTCGTCCC[G/A]
CGTCACCACAACGCGATTTGTGATCCCACCCGCATTTTCAATCTGCGACATATGTACATTTCTGCGATTTCTTCCTATGCAAGGATATAAATGTAAATTA

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	56.40%	39.40%	1.88%	2.29%	NA
All Indica	2759	86.00%	7.20%	2.79%	3.91%	NA
All Japonica	1512	2.50%	96.80%	0.66%	0.00%	NA
Aus	269	78.40%	21.60%	0.00%	0.00%	NA
Indica I	595	90.40%	4.90%	0.50%	4.20%	NA
Indica II	465	77.40%	4.30%	9.46%	8.82%	NA
Indica III	913	90.10%	7.90%	0.77%	1.20%	NA
Indica Intermediate	786	83.10%	10.10%	2.93%	3.94%	NA
Temperate Japonica	767	2.10%	97.80%	0.13%	0.00%	NA
Tropical Japonica	504	2.00%	98.00%	0.00%	0.00%	NA
Japonica Intermediate	241	5.00%	91.30%	3.73%	0.00%	NA
VI/Aromatic	96	14.60%	85.40%	0.00%	0.00%	NA
Intermediate	90	31.10%	66.70%	2.22%	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
vg1218704534	C -> DEL	N	N	silent_mutation	Average:53.478; most accessible tissue: Zhenshan97 panicle, score: 71.253	N	N	N	N
vg1218704534	C -> T	LOC_Os12g31110-LOC_Os12g31120	intergenic_region ; MODIFIER	silent_mutation	Average:53.478; most accessible tissue: Zhenshan97 panicle, score: 71.253	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1218704534	NA	1.58E-20	mr1254	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
vg1218704534	1.26E-07	NA	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
vg1218704534	1.41E-07	3.32E-10	mr1458	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
vg1218704534	NA	8.16E-06	mr1681	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
vg1218704534	NA	7.58E-07	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
vg1218704534	4.85E-08	NA	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
vg1218704534	4.87E-13	1.31E-13	mr1458_2	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