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Detailed information for vg1217569213:

Variant ID: vg1217569213 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 17569213
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.99, others allele: 0.00, population size: 103. )

Flanking Sequence (100 bp) in Reference Genome:

ATAGTCAAATATTATTAAAAAGTCAATGGGGTCATACATTAAAAATACGGAGGGAGTACTCGTTAAAATTCTGGCTTCGTCACTGGTTGCTACTAAGTAG[T/C]
ACCGCCTTAAGAGCAGATACAATAGCAGGCTATAAACCAGCTATAAACATATTTTAAAGAGATAAAAGAAGAGAGAAGAGCAGCGGACTACAGATATGTA

Reverse complement sequence

TACATATCTGTAGTCCGCTGCTCTTCTCTCTTCTTTTATCTCTTTAAAATATGTTTATAGCTGGTTTATAGCCTGCTATTGTATCTGCTCTTAAGGCGGT[A/G]
CTACTTAGTAGCAACCAGTGACGAAGCCAGAATTTTAACGAGTACTCCCTCCGTATTTTTAATGTATGACCCCATTGACTTTTTAATAATATTTGACTAT

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	70.70%	29.20%	0.15%	0.00%	NA
All Indica	2759	58.10%	41.70%	0.14%	0.00%	NA
All Japonica	1512	88.00%	12.00%	0.07%	0.00%	NA
Aus	269	92.20%	7.40%	0.37%	0.00%	NA
Indica I	595	23.50%	76.50%	0.00%	0.00%	NA
Indica II	465	83.20%	16.80%	0.00%	0.00%	NA
Indica III	913	68.80%	31.10%	0.11%	0.00%	NA
Indica Intermediate	786	57.10%	42.50%	0.38%	0.00%	NA
Temperate Japonica	767	95.20%	4.70%	0.13%	0.00%	NA
Tropical Japonica	504	78.40%	21.60%	0.00%	0.00%	NA
Japonica Intermediate	241	85.10%	14.90%	0.00%	0.00%	NA
VI/Aromatic	96	91.70%	8.30%	0.00%	0.00%	NA
Intermediate	90	76.70%	22.20%	1.11%	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
vg1217569213	T -> C	LOC_Os12g29520.1	downstream_gene_variant ; 2324.0bp to feature; MODIFIER	silent_mutation	Average:30.603; most accessible tissue: Callus, score: 70.108	N	N	N	N
vg1217569213	T -> C	LOC_Os12g29520.2	downstream_gene_variant ; 2324.0bp to feature; MODIFIER	silent_mutation	Average:30.603; most accessible tissue: Callus, score: 70.108	N	N	N	N
vg1217569213	T -> C	LOC_Os12g29520.3	downstream_gene_variant ; 2324.0bp to feature; MODIFIER	silent_mutation	Average:30.603; most accessible tissue: Callus, score: 70.108	N	N	N	N
vg1217569213	T -> C	LOC_Os12g29520.4	downstream_gene_variant ; 2324.0bp to feature; MODIFIER	silent_mutation	Average:30.603; most accessible tissue: Callus, score: 70.108	N	N	N	N
vg1217569213	T -> C	LOC_Os12g29520.5	downstream_gene_variant ; 2324.0bp to feature; MODIFIER	silent_mutation	Average:30.603; most accessible tissue: Callus, score: 70.108	N	N	N	N
vg1217569213	T -> C	LOC_Os12g29510-LOC_Os12g29520	intergenic_region ; MODIFIER	silent_mutation	Average:30.603; most accessible tissue: Callus, score: 70.108	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1217569213	2.45E-07	5.57E-09	mr1388	Jap_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
vg1217569213	9.42E-07	9.41E-07	mr1601	Jap_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
vg1217569213	NA	3.88E-07	mr1835	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