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Detailed information for vg1214618940:

Variant ID: vg1214618940 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 14618940
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, T: 0.01, others allele: 0.00, population size: 124. )

Flanking Sequence (100 bp) in Reference Genome:

CTGTGACGGGCCTTTACTTTTAGGGCCGTCACAGGTAGATCGCCTGTGACAGCTTCTAACTACGGAGACCATCACCTCTGACGGCCTTTATTTAAAGGGC[C/T]
GTCAGAGATGAGTCACCTTTGACGGGTCCCAACTCGCCCTAGGCAAGCGGAGACCAACACCATGAGAATATATGACGAAATAAAGCCATGTAGTAGATGA

Reverse complement sequence

TCATCTACTACATGGCTTTATTTCGTCATATATTCTCATGGTGTTGGTCTCCGCTTGCCTAGGGCGAGTTGGGACCCGTCAAAGGTGACTCATCTCTGAC[G/A]
GCCCTTTAAATAAAGGCCGTCAGAGGTGATGGTCTCCGTAGTTAGAAGCTGTCACAGGCGATCTACCTGTGACGGCCCTAAAAGTAAAGGCCCGTCACAG

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	73.80%	9.00%	0.17%	17.03%	NA
All Indica	2759	56.30%	14.90%	0.29%	28.56%	NA
All Japonica	1512	99.50%	0.20%	0.00%	0.26%	NA
Aus	269	99.60%	0.00%	0.00%	0.37%	NA
Indica I	595	60.20%	21.30%	0.17%	18.32%	NA
Indica II	465	67.30%	2.20%	0.65%	29.89%	NA
Indica III	913	45.30%	16.40%	0.22%	38.01%	NA
Indica Intermediate	786	59.40%	15.80%	0.25%	24.55%	NA
Temperate Japonica	767	99.60%	0.00%	0.00%	0.39%	NA
Tropical Japonica	504	99.40%	0.60%	0.00%	0.00%	NA
Japonica Intermediate	241	99.60%	0.00%	0.00%	0.41%	NA
VI/Aromatic	96	88.50%	2.10%	0.00%	9.38%	NA
Intermediate	90	87.80%	8.90%	0.00%	3.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1214618940	C -> DEL	N	N	silent_mutation	Average:39.151; most accessible tissue: Zhenshan97 young leaf, score: 50.0	N	N	N	N
vg1214618940	C -> T	LOC_Os12g25340.1	downstream_gene_variant ; 902.0bp to feature; MODIFIER	silent_mutation	Average:39.151; most accessible tissue: Zhenshan97 young leaf, score: 50.0	N	N	N	N
vg1214618940	C -> T	LOC_Os12g25340-LOC_Os12g25350	intergenic_region ; MODIFIER	silent_mutation	Average:39.151; most accessible tissue: Zhenshan97 young leaf, score: 50.0	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1214618940	5.00E-08	5.00E-08	mr1540	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
vg1214618940	5.02E-06	6.45E-07	mr1732	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