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Detailed information for vg1201206550:

Variant ID: vg1201206550 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 1206550
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.66, T: 0.34, others allele: 0.00, population size: 50. )

Flanking Sequence (100 bp) in Reference Genome:

ATGTGTTTGGCGCTGAGGCGACGGCCTATTTTTGGTTGAAGTTTTTGGCAGGGGTTAGTTTCGAAATAAGTTTTCCAAAAGGGTCAATTTGTCAAAAAAA[T/C]
GGCAGATTGCGTGTAAATTGCGAGACGAATCTTTTAAGTCTAATTGCGCCATGATTTGACAACGTGGTGCTACAATAAACATTTGCTAATGACGGATTAA

Reverse complement sequence

TTAATCCGTCATTAGCAAATGTTTATTGTAGCACCACGTTGTCAAATCATGGCGCAATTAGACTTAAAAGATTCGTCTCGCAATTTACACGCAATCTGCC[A/G]
TTTTTTTGACAAATTGACCCTTTTGGAAAACTTATTTCGAAACTAACCCCTGCCAAAAACTTCAACCAAAAATAGGCCGTCGCCTCAGCGCCAAACACAT

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	43.20%	30.20%	4.57%	22.11%	NA
All Indica	2759	23.70%	41.80%	5.36%	29.21%	NA
All Japonica	1512	85.20%	13.00%	1.59%	0.26%	NA
Aus	269	0.70%	1.90%	14.50%	82.90%	NA
Indica I	595	52.10%	15.50%	7.23%	25.21%	NA
Indica II	465	10.30%	78.50%	4.73%	6.45%	NA
Indica III	913	17.30%	37.10%	2.30%	43.26%	NA
Indica Intermediate	786	17.40%	45.30%	7.89%	29.39%	NA
Temperate Japonica	767	87.40%	10.30%	2.09%	0.26%	NA
Tropical Japonica	504	78.00%	20.60%	0.99%	0.40%	NA
Japonica Intermediate	241	93.40%	5.40%	1.24%	0.00%	NA
VI/Aromatic	96	49.00%	46.90%	0.00%	4.17%	NA
Intermediate	90	55.60%	30.00%	5.56%	8.89%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1201206550	T -> C	LOC_Os12g03150.1	upstream_gene_variant ; 4348.0bp to feature; MODIFIER	silent_mutation	Average:45.066; most accessible tissue: Zhenshan97 panicle, score: 65.386	N	N	N	N
vg1201206550	T -> C	LOC_Os12g03160.1	downstream_gene_variant ; 328.0bp to feature; MODIFIER	silent_mutation	Average:45.066; most accessible tissue: Zhenshan97 panicle, score: 65.386	N	N	N	N
vg1201206550	T -> C	LOC_Os12g03160-LOC_Os12g03170	intergenic_region ; MODIFIER	silent_mutation	Average:45.066; most accessible tissue: Zhenshan97 panicle, score: 65.386	N	N	N	N
vg1201206550	T -> DEL	N	N	silent_mutation	Average:45.066; most accessible tissue: Zhenshan97 panicle, score: 65.386	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1201206550	NA	8.59E-06	mr1219	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
vg1201206550	NA	8.32E-07	mr1245	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