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Detailed information for vg1121374782:

Variant ID: vg1121374782 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 21374782
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.81, T: 0.19, others allele: 0.00, population size: 94. )

Flanking Sequence (100 bp) in Reference Genome:

ACAGAAGGGCGGCCAAGGCACTCCTCGATGAGGTGAAGCAAACGGCAGTGACGGCGCGACTTGAGGTGGCTAGGAGCGGCGGTGGTGGCCGACCGAAGTG[C/T]
AGAACGGCAGCGGCACTAGGGGATTCACAGTGGAGATGGTGTTTCGTGGGTGGAAGGTAGAAGTGGAGTGGGTGCTGGGGTGCGGAGCGGCATGGCGAAG

Reverse complement sequence

CTTCGCCATGCCGCTCCGCACCCCAGCACCCACTCCACTTCTACCTTCCACCCACGAAACACCATCTCCACTGTGAATCCCCTAGTGCCGCTGCCGTTCT[G/A]
CACTTCGGTCGGCCACCACCGCCGCTCCTAGCCACCTCAAGTCGCGCCGTCACTGCCGTTTGCTTCACCTCATCGAGGAGTGCCTTGGCCGCCCTTCTGT

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	65.80%	32.40%	0.17%	1.67%	NA
All Indica	2759	54.20%	45.10%	0.25%	0.51%	NA
All Japonica	1512	89.90%	9.10%	0.07%	0.93%	NA
Aus	269	40.50%	41.30%	0.00%	18.22%	NA
Indica I	595	52.80%	46.90%	0.17%	0.17%	NA
Indica II	465	57.40%	39.60%	0.86%	2.15%	NA
Indica III	913	52.80%	47.00%	0.11%	0.11%	NA
Indica Intermediate	786	54.80%	44.80%	0.13%	0.25%	NA
Temperate Japonica	767	94.00%	4.30%	0.00%	1.69%	NA
Tropical Japonica	504	83.90%	15.90%	0.00%	0.20%	NA
Japonica Intermediate	241	89.20%	10.40%	0.41%	0.00%	NA
VI/Aromatic	96	88.50%	11.50%	0.00%	0.00%	NA
Intermediate	90	70.00%	27.80%	0.00%	2.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1121374782	C -> T	LOC_Os11g36300.1	upstream_gene_variant ; 92.0bp to feature; MODIFIER	silent_mutation	Average:70.949; most accessible tissue: Zhenshan97 young leaf, score: 89.772	N	N	N	N
vg1121374782	C -> T	LOC_Os11g36290.1	downstream_gene_variant ; 2331.0bp to feature; MODIFIER	silent_mutation	Average:70.949; most accessible tissue: Zhenshan97 young leaf, score: 89.772	N	N	N	N
vg1121374782	C -> T	LOC_Os11g36290-LOC_Os11g36300	intergenic_region ; MODIFIER	silent_mutation	Average:70.949; most accessible tissue: Zhenshan97 young leaf, score: 89.772	N	N	N	N
vg1121374782	C -> DEL	N	N	silent_mutation	Average:70.949; most accessible tissue: Zhenshan97 young leaf, score: 89.772	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1121374782	1.80E-06	9.64E-09	mr1164_2	Jap_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
vg1121374782	NA	6.13E-06	mr1561_2	Jap_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