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Detailed information for vg1211153360:

Variant ID: vg1211153360 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 11153360
Reference Allele: A	Alternative Allele: C
Primary Allele: A	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 113. )

Flanking Sequence (100 bp) in Reference Genome:

GGGAATCTACGAACTATACCAGCTGGACGCCCTCGACGTCTCTATTATGAGTTGCTGGATTTTGTAAGTATATCGTTCAGTTAGATTTCTTACTACGTCT[A/C]
CTTTAATTAATTAGGTCCTTGTATATAAGTAGACTCTATATATAATATATACTCCCTTTTATTGTTGTAGAATGGAGATCCAAAGGGCCCGACGGCAGGG

Reverse complement sequence

CCCTGCCGTCGGGCCCTTTGGATCTCCATTCTACAACAATAAAAGGGAGTATATATTATATATAGAGTCTACTTATATACAAGGACCTAATTAATTAAAG[T/G]
AGACGTAGTAAGAAATCTAACTGAACGATATACTTACAAAATCCAGCAACTCATAATAGAGACGTCGAGGGCGTCCAGCTGGTATAGTTCGTAGATTCCC

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	15.90%	14.40%	4.89%	64.81%	NA
All Indica	2759	2.20%	23.20%	5.15%	69.41%	NA
All Japonica	1512	44.00%	1.20%	0.99%	53.84%	NA
Aus	269	0.40%	4.10%	25.28%	70.26%	NA
Indica I	595	1.70%	3.90%	4.54%	89.92%	NA
Indica II	465	3.20%	36.10%	2.80%	57.85%	NA
Indica III	913	0.30%	26.90%	5.37%	67.36%	NA
Indica Intermediate	786	4.30%	25.80%	6.74%	63.10%	NA
Temperate Japonica	767	78.00%	0.50%	0.52%	20.99%	NA
Tropical Japonica	504	2.20%	2.00%	1.59%	94.25%	NA
Japonica Intermediate	241	23.20%	1.70%	1.24%	73.86%	NA
VI/Aromatic	96	0.00%	2.10%	1.04%	96.88%	NA
Intermediate	90	24.40%	12.20%	5.56%	57.78%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1211153360	A -> C	LOC_Os12g19230.1	upstream_gene_variant ; 3436.0bp to feature; MODIFIER	silent_mutation	Average:7.119; most accessible tissue: Callus, score: 16.832	N	N	N	N
vg1211153360	A -> C	LOC_Os12g19200.1	downstream_gene_variant ; 4422.0bp to feature; MODIFIER	silent_mutation	Average:7.119; most accessible tissue: Callus, score: 16.832	N	N	N	N
vg1211153360	A -> C	LOC_Os12g19210.1	downstream_gene_variant ; 1392.0bp to feature; MODIFIER	silent_mutation	Average:7.119; most accessible tissue: Callus, score: 16.832	N	N	N	N
vg1211153360	A -> C	LOC_Os12g19220.1	intron_variant ; MODIFIER	silent_mutation	Average:7.119; most accessible tissue: Callus, score: 16.832	N	N	N	N
vg1211153360	A -> DEL	N	N	silent_mutation	Average:7.119; most accessible tissue: Callus, score: 16.832	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1211153360	NA	6.32E-09	mr1446_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
vg1211153360	NA	1.74E-06	mr1446_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