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Detailed information for vg1119157316:

Variant ID: vg1119157316 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 19157316
Reference Allele: T	Alternative Allele: G
Primary Allele: T	Secondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.71, T: 0.29, others allele: 0.00, population size: 77. )

Flanking Sequence (100 bp) in Reference Genome:

TTAAAGTTCGTTTGGGTTAACCAAAGCGAACGAACTTGCTCATACAAAATTAAACAAGTCGGCAGCTCTGCTTGATGCGAAATTAAATGAAAATTAAACC[T/G]
CTTGCAAGTTATATATATGAACTCATGAAGTGAGGTTGTGTGTCATGGACTCATGGTGTATGTCACCGAGGAGGCGGCACAACTGCGCGCGGACCAGGAG

Reverse complement sequence

CTCCTGGTCCGCGCGCAGTTGTGCCGCCTCCTCGGTGACATACACCATGAGTCCATGACACACAACCTCACTTCATGAGTTCATATATATAACTTGCAAG[A/C]
GGTTTAATTTTCATTTAATTTCGCATCAAGCAGAGCTGCCGACTTGTTTAATTTTGTATGAGCAAGTTCGTTCGCTTTGGTTAACCCAAACGAACTTTAA

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	45.00%	4.90%	0.70%	49.39%	NA
All Indica	2759	23.20%	5.40%	0.98%	70.46%	NA
All Japonica	1512	90.40%	0.20%	0.20%	9.19%	NA
Aus	269	4.10%	25.70%	0.37%	69.89%	NA
Indica I	595	59.30%	1.70%	0.67%	38.32%	NA
Indica II	465	4.50%	6.70%	0.86%	87.96%	NA
Indica III	913	11.50%	5.00%	0.99%	82.48%	NA
Indica Intermediate	786	20.50%	7.80%	1.27%	70.48%	NA
Temperate Japonica	767	94.30%	0.10%	0.13%	5.48%	NA
Tropical Japonica	504	87.10%	0.40%	0.20%	12.30%	NA
Japonica Intermediate	241	85.10%	0.00%	0.41%	14.52%	NA
VI/Aromatic	96	79.20%	2.10%	0.00%	18.75%	NA
Intermediate	90	37.80%	10.00%	2.22%	50.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1119157316	T -> DEL	N	N	silent_mutation	Average:34.792; most accessible tissue: Callus, score: 67.004	N	N	N	N
vg1119157316	T -> G	LOC_Os11g32440.1	downstream_gene_variant ; 3444.0bp to feature; MODIFIER	silent_mutation	Average:34.792; most accessible tissue: Callus, score: 67.004	N	N	N	N
vg1119157316	T -> G	LOC_Os11g32460.1	downstream_gene_variant ; 4921.0bp to feature; MODIFIER	silent_mutation	Average:34.792; most accessible tissue: Callus, score: 67.004	N	N	N	N
vg1119157316	T -> G	LOC_Os11g32440-LOC_Os11g32460	intergenic_region ; MODIFIER	silent_mutation	Average:34.792; most accessible tissue: Callus, score: 67.004	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1119157316	NA	6.40E-06	mr1354	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
vg1119157316	NA	4.77E-08	mr1138_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
vg1119157316	NA	3.13E-11	mr1354_2	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