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Detailed information for vg1219427349:

Variant ID: vg1219427349 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 19427349
Reference Allele: T	Alternative Allele: A
Primary Allele: T	Secondary Allele: A

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 295. )

Flanking Sequence (100 bp) in Reference Genome:

GCATCTCAGAATTTGTCATTGAATTTCACCTCGAGTGTGAGTTATGTTATGGGGCCACATGTAATTGAAAGGGTGCTACATCATTGTATGCCACATAACT[T/A]
ATGGAAAATCCTTGTTTCATCAATATAACATTGAACCTTGCATATCTATAGATGAAAGGTAATGCAATTAATACCGAACCTTTCATGCAGTAGGATATAA

Reverse complement sequence

TTATATCCTACTGCATGAAAGGTTCGGTATTAATTGCATTACCTTTCATCTATAGATATGCAAGGTTCAATGTTATATTGATGAAACAAGGATTTTCCAT[A/T]
AGTTATGTGGCATACAATGATGTAGCACCCTTTCAATTACATGTGGCCCCATAACATAACTCACACTCGAGGTGAAATTCAATGACAAATTCTGAGATGC

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	92.00%	8.00%	0.00%	0.00%	NA
All Indica	2759	90.90%	9.10%	0.00%	0.00%	NA
All Japonica	1512	99.90%	0.10%	0.00%	0.00%	NA
Aus	269	56.10%	43.90%	0.00%	0.00%	NA
Indica I	595	80.30%	19.70%	0.00%	0.00%	NA
Indica II	465	96.60%	3.40%	0.00%	0.00%	NA
Indica III	913	93.10%	6.90%	0.00%	0.00%	NA
Indica Intermediate	786	93.00%	7.00%	0.00%	0.00%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	99.80%	0.20%	0.00%	0.00%	NA
Japonica Intermediate	241	99.60%	0.40%	0.00%	0.00%	NA
VI/Aromatic	96	99.00%	1.00%	0.00%	0.00%	NA
Intermediate	90	94.40%	5.60%	0.00%	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
vg1219427349	T -> A	LOC_Os12g32190.1	downstream_gene_variant ; 1578.0bp to feature; MODIFIER	silent_mutation	Average:42.121; most accessible tissue: Zhenshan97 young leaf, score: 53.314	N	N	N	N
vg1219427349	T -> A	LOC_Os12g32190.2	downstream_gene_variant ; 1578.0bp to feature; MODIFIER	silent_mutation	Average:42.121; most accessible tissue: Zhenshan97 young leaf, score: 53.314	N	N	N	N
vg1219427349	T -> A	LOC_Os12g32180.1	intron_variant ; MODIFIER	silent_mutation	Average:42.121; most accessible tissue: Zhenshan97 young leaf, score: 53.314	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1219427349	4.08E-07	NA	mr1244	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