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Detailed information for vg1219228902:

Variant ID: vg1219228902 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 19228902
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TGTCGAGAAATCAACAACCATGCATTCAATGATGTTAAGGAAATAAATGCATATGGAAAGATGCCTGCTTTTAACTTTTGGAAAAAGTACGAATTACACC[C/T]
CTGAACTATTACGATCGATCGAATTACCCTCCTAAACTCAAATACTAGATGTTTTACATCCTGAATTATTCAAACCGGATAATTAACCCTCTGGCTCAAT

Reverse complement sequence

ATTGAGCCAGAGGGTTAATTATCCGGTTTGAATAATTCAGGATGTAAAACATCTAGTATTTGAGTTTAGGAGGGTAATTCGATCGATCGTAATAGTTCAG[G/A]
GGTGTAATTCGTACTTTTTCCAAAAGTTAAAAGCAGGCATCTTTCCATATGCATTTATTTCCTTAACATCATTGAATGCATGGTTGTTGATTTCTCGACA

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	41.40%	4.10%	1.50%	52.96%	NA
All Indica	2759	12.10%	5.90%	2.46%	79.52%	NA
All Japonica	1512	96.80%	0.10%	0.07%	2.98%	NA
Aus	269	4.80%	10.40%	0.00%	84.76%	NA
Indica I	595	15.10%	0.30%	3.36%	81.18%	NA
Indica II	465	4.70%	18.50%	1.29%	75.48%	NA
Indica III	913	11.60%	5.10%	2.19%	81.05%	NA
Indica Intermediate	786	14.90%	3.40%	2.80%	78.88%	NA
Temperate Japonica	767	98.40%	0.00%	0.13%	1.43%	NA
Tropical Japonica	504	97.60%	0.00%	0.00%	2.38%	NA
Japonica Intermediate	241	90.00%	0.80%	0.00%	9.13%	NA
VI/Aromatic	96	83.30%	4.20%	0.00%	12.50%	NA
Intermediate	90	71.10%	0.00%	2.22%	26.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1219228902	C -> DEL	N	N	silent_mutation	Average:9.699; most accessible tissue: Callus, score: 46.106	N	N	N	N
vg1219228902	C -> T	LOC_Os12g31920.1	upstream_gene_variant ; 4399.0bp to feature; MODIFIER	silent_mutation	Average:9.699; most accessible tissue: Callus, score: 46.106	N	N	N	N
vg1219228902	C -> T	LOC_Os12g31910.1	intron_variant ; MODIFIER	silent_mutation	Average:9.699; most accessible tissue: Callus, score: 46.106	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1219228902	2.45E-06	1.39E-08	mr1268	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
vg1219228902	NA	1.58E-06	mr1268	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