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Detailed information for vg1218936276:

Variant ID: vg1218936276 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 18936276
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.97, T: 0.05, others allele: 0.00, population size: 86. )

Flanking Sequence (100 bp) in Reference Genome:

TCATTTTATGTGGACCGGTCAGACCGGGCTCTGGTAGCCGGTCAGACCGGCGTGTATCGCACGGTCAGACCGGCGCACTCCGCGGTCTGACCGGCCGACA[C/T]
TGTGTCGGTTTCGGTTTCGGGTTGTTTATTTGGATATCCGAGTTTATTCCATGATTATGACTTCTAGATGGATACTATACATATGTAATACTATTGTTTG

Reverse complement sequence

CAAACAATAGTATTACATATGTATAGTATCCATCTAGAAGTCATAATCATGGAATAAACTCGGATATCCAAATAAACAACCCGAAACCGAAACCGACACA[G/A]
TGTCGGCCGGTCAGACCGCGGAGTGCGCCGGTCTGACCGTGCGATACACGCCGGTCTGACCGGCTACCAGAGCCCGGTCTGACCGGTCCACATAAAATGA

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	48.30%	41.50%	5.78%	4.49%	NA
All Indica	2759	21.20%	62.50%	8.74%	7.58%	NA
All Japonica	1512	98.60%	1.20%	0.13%	0.07%	NA
Aus	269	23.00%	71.00%	5.95%	0.00%	NA
Indica I	595	12.40%	66.60%	16.13%	4.87%	NA
Indica II	465	24.30%	58.50%	7.74%	9.46%	NA
Indica III	913	22.60%	63.90%	4.49%	9.09%	NA
Indica Intermediate	786	24.30%	60.30%	8.65%	6.74%	NA
Temperate Japonica	767	99.20%	0.80%	0.00%	0.00%	NA
Tropical Japonica	504	99.20%	0.60%	0.20%	0.00%	NA
Japonica Intermediate	241	95.40%	3.70%	0.41%	0.41%	NA
VI/Aromatic	96	80.20%	9.40%	10.42%	0.00%	NA
Intermediate	90	74.40%	18.90%	4.44%	2.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1218936276	C -> DEL	N	N	silent_mutation	Average:35.55; most accessible tissue: Zhenshan97 panicle, score: 57.341	N	N	N	N
vg1218936276	C -> T	LOC_Os12g31485.1	upstream_gene_variant ; 239.0bp to feature; MODIFIER	silent_mutation	Average:35.55; most accessible tissue: Zhenshan97 panicle, score: 57.341	N	N	N	N
vg1218936276	C -> T	LOC_Os12g31470.1	downstream_gene_variant ; 4784.0bp to feature; MODIFIER	silent_mutation	Average:35.55; most accessible tissue: Zhenshan97 panicle, score: 57.341	N	N	N	N
vg1218936276	C -> T	LOC_Os12g31480.1	downstream_gene_variant ; 150.0bp to feature; MODIFIER	silent_mutation	Average:35.55; most accessible tissue: Zhenshan97 panicle, score: 57.341	N	N	N	N
vg1218936276	C -> T	LOC_Os12g31490.1	downstream_gene_variant ; 2438.0bp to feature; MODIFIER	silent_mutation	Average:35.55; most accessible tissue: Zhenshan97 panicle, score: 57.341	N	N	N	N
vg1218936276	C -> T	LOC_Os12g31480-LOC_Os12g31485	intergenic_region ; MODIFIER	silent_mutation	Average:35.55; most accessible tissue: Zhenshan97 panicle, score: 57.341	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1218936276	NA	1.74E-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
vg1218936276	8.96E-06	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
vg1218936276	2.52E-08	5.68E-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