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Detailed information for vg0411135218:

Variant ID: vg0411135218 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 11135218
Reference Allele: G	Alternative Allele: T
Primary Allele: G	Secondary Allele: T

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, others allele: 0.00, population size: 126. )

Flanking Sequence (100 bp) in Reference Genome:

TTCGAGTTTGTCTTCTTTTGATTGGATGAAACAGGTTGTTTTAAATCGACCACGTGATGAGCACCATATGGAAAAACCGAGGACGGTTTTCCGTGAAGAA[G/T]
GGGAGGATGATGGGACCATGGCTACTATGGATACAACCATTGCTCACATCATGGATGAACAGCATGATATCAAGTTCAAGTCCTCCAAGTGCTGGAATCC

Reverse complement sequence

GGATTCCAGCACTTGGAGGACTTGAACTTGATATCATGCTGTTCATCCATGATGTGAGCAATGGTTGTATCCATAGTAGCCATGGTCCCATCATCCTCCC[C/A]
TTCTTCACGGAAAACCGTCCTCGGTTTTTCCATATGGTGCTCATCACGTGGTCGATTTAAAACAACCTGTTTCATCCAATCAAAAGAAGACAAACTCGAA

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	73.30%	14.20%	6.09%	6.41%	NA
All Indica	2759	54.60%	24.10%	10.33%	10.98%	NA
All Japonica	1512	100.00%	0.00%	0.00%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	25.20%	38.50%	22.18%	14.12%	NA
Indica II	465	75.90%	14.00%	4.52%	5.59%	NA
Indica III	913	59.80%	19.70%	8.11%	12.38%	NA
Indica Intermediate	786	58.30%	24.20%	7.38%	10.18%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	90.00%	6.70%	3.33%	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
vg0411135218	G -> DEL	N	N	silent_mutation	Average:33.891; most accessible tissue: Minghui63 root, score: 49.234	N	N	N	N
vg0411135218	G -> T	LOC_Os04g19970.1	upstream_gene_variant ; 1650.0bp to feature; MODIFIER	silent_mutation	Average:33.891; most accessible tissue: Minghui63 root, score: 49.234	N	N	N	N
vg0411135218	G -> T	LOC_Os04g19960.1	downstream_gene_variant ; 3716.0bp to feature; MODIFIER	silent_mutation	Average:33.891; most accessible tissue: Minghui63 root, score: 49.234	N	N	N	N
vg0411135218	G -> T	LOC_Os04g19980.1	downstream_gene_variant ; 857.0bp to feature; MODIFIER	silent_mutation	Average:33.891; most accessible tissue: Minghui63 root, score: 49.234	N	N	N	N
vg0411135218	G -> T	LOC_Os04g19970-LOC_Os04g19980	intergenic_region ; MODIFIER	silent_mutation	Average:33.891; most accessible tissue: Minghui63 root, score: 49.234	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0411135218	2.64E-06	NA	mr1063_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