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Detailed information for vg1219748144:

Variant ID: vg1219748144 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 19748144
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: 72. )

Flanking Sequence (100 bp) in Reference Genome:

AAACAAAACATCCATTCAGGATAAGAACCTAGGTAAGTAAATATGCAACAGTTGAGGTGGAACTGGTTTCTTAAATAAACCATAGAAGTAGCATTGCATT[T/A]
TTTAATAAACTTGCCAGATATGAACTCAACCAAGTCAGATATGCCATTAACAAACCTACATAGCCATTAACAAACAAACGCCAAACATTAATTTCCTGAT

Reverse complement sequence

ATCAGGAAATTAATGTTTGGCGTTTGTTTGTTAATGGCTATGTAGGTTTGTTAATGGCATATCTGACTTGGTTGAGTTCATATCTGGCAAGTTTATTAAA[A/T]
AATGCAATGCTACTTCTATGGTTTATTTAAGAAACCAGTTCCACCTCAACTGTTGCATATTTACTTACCTAGGTTCTTATCCTGAATGGATGTTTTGTTT

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	46.50%	33.50%	1.71%	18.30%	NA
All Indica	2759	19.00%	49.90%	2.57%	28.45%	NA
All Japonica	1512	96.80%	1.20%	0.26%	1.72%	NA
Aus	269	24.50%	63.20%	1.86%	10.41%	NA
Indica I	595	6.60%	71.60%	2.52%	19.33%	NA
Indica II	465	6.90%	54.60%	2.80%	35.70%	NA
Indica III	913	30.10%	32.60%	1.97%	35.27%	NA
Indica Intermediate	786	22.80%	50.90%	3.18%	23.16%	NA
Temperate Japonica	767	98.30%	0.10%	0.13%	1.43%	NA
Tropical Japonica	504	96.20%	1.00%	0.20%	2.58%	NA
Japonica Intermediate	241	93.40%	5.00%	0.83%	0.83%	NA
VI/Aromatic	96	78.10%	7.30%	0.00%	14.58%	NA
Intermediate	90	74.40%	11.10%	1.11%	13.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1219748144	T -> DEL	N	N	silent_mutation	Average:18.714; most accessible tissue: Callus, score: 48.423	N	N	N	N
vg1219748144	T -> A	LOC_Os12g32700.1	intron_variant ; MODIFIER	silent_mutation	Average:18.714; most accessible tissue: Callus, score: 48.423	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1219748144	NA	6.18E-07	mr1215	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
vg1219748144	NA	1.76E-07	mr1220	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
vg1219748144	NA	1.42E-06	mr1450	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
vg1219748144	NA	2.32E-09	mr1575	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
vg1219748144	NA	3.64E-06	mr1646	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
vg1219748144	NA	4.54E-08	mr1779	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
vg1219748144	NA	3.99E-06	mr1832	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
vg1219748144	NA	4.04E-06	mr1884	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
vg1219748144	NA	2.09E-06	mr1992	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
vg1219748144	NA	3.21E-07	mr1205_2	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
vg1219748144	7.82E-06	NA	mr1269_2	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
vg1219748144	9.22E-06	NA	mr1746_2	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
vg1219748144	NA	6.89E-06	mr1746_2	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