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Detailed information for vg1217854218:

Variant ID: vg1217854218 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 17854218
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GCGAAGCACACAAGCAAAGCTACAACCCTATAAAGAAGCAATAACAATACATAAAAAGATAGCACAGGGTTCTTTAGGTTATAACAAACATTAAAAGACT[T/C]
GAACGAGTCGATTCGGAGTTCGTATGACCAAGATATGGTCATCCAAAGTTTAATGCTGTTATATGGAGATTTGCGGATTATTATAATTAAGCTTTGCAAC

Reverse complement sequence

GTTGCAAAGCTTAATTATAATAATCCGCAAATCTCCATATAACAGCATTAAACTTTGGATGACCATATCTTGGTCATACGAACTCCGAATCGACTCGTTC[A/G]
AGTCTTTTAATGTTTGTTATAACCTAAAGAACCCTGTGCTATCTTTTTATGTATTGTTATTGCTTCTTTATAGGGTTGTAGCTTTGCTTGTGTGCTTCGC

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	50.90%	9.80%	6.26%	33.03%	NA
All Indica	2759	37.60%	15.40%	9.21%	37.73%	NA
All Japonica	1512	75.20%	0.40%	1.12%	23.28%	NA
Aus	269	46.80%	7.40%	4.46%	41.26%	NA
Indica I	595	51.80%	8.10%	7.06%	33.11%	NA
Indica II	465	44.30%	4.50%	10.54%	40.65%	NA
Indica III	913	24.10%	20.70%	10.73%	44.47%	NA
Indica Intermediate	786	38.70%	21.40%	8.27%	31.68%	NA
Temperate Japonica	767	97.80%	0.10%	0.26%	1.83%	NA
Tropical Japonica	504	48.00%	0.40%	1.79%	49.80%	NA
Japonica Intermediate	241	60.20%	1.20%	2.49%	36.10%	NA
VI/Aromatic	96	47.90%	1.00%	8.33%	42.71%	NA
Intermediate	90	65.60%	11.10%	5.56%	17.78%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1217854218	T -> C	LOC_Os12g29860.1	upstream_gene_variant ; 714.0bp to feature; MODIFIER	silent_mutation	Average:8.214; most accessible tissue: Callus, score: 16.377	N	N	N	N
vg1217854218	T -> C	LOC_Os12g29850.1	downstream_gene_variant ; 1844.0bp to feature; MODIFIER	silent_mutation	Average:8.214; most accessible tissue: Callus, score: 16.377	N	N	N	N
vg1217854218	T -> C	LOC_Os12g29850-LOC_Os12g29860	intergenic_region ; MODIFIER	silent_mutation	Average:8.214; most accessible tissue: Callus, score: 16.377	N	N	N	N
vg1217854218	T -> DEL	N	N	silent_mutation	Average:8.214; most accessible tissue: Callus, score: 16.377	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1217854218	4.10E-06	4.10E-06	mr1321	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
vg1217854218	7.84E-06	7.84E-06	mr1323	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