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Detailed information for vg1102378145:

Variant ID: vg1102378145 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 2378145
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 272. )

Flanking Sequence (100 bp) in Reference Genome:

CATGCATCCGTTTGACCTTAATTTGAGCGAATTATTCTTTTTCAATCCGAGTTTTGTTACAGACTAGAATAAACTCATTGGATATATTTGAAGAAATTCT[G/A]
ACCATTGGTTGAAATGGTCTGTAAATTGCGAACAGTTATTATAACTGAACGTAGAAAAATGATAATTAAAACAAAAATATGTGATGATAGGGCATGAATT

Reverse complement sequence

AATTCATGCCCTATCATCACATATTTTTGTTTTAATTATCATTTTTCTACGTTCAGTTATAATAACTGTTCGCAATTTACAGACCATTTCAACCAATGGT[C/T]
AGAATTTCTTCAAATATATCCAATGAGTTTATTCTAGTCTGTAACAAAACTCGGATTGAAAAAGAATAATTCGCTCAAATTAAGGTCAAACGGATGCATG

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	77.50%	7.30%	2.96%	12.17%	NA
All Indica	2759	66.40%	11.80%	3.52%	18.30%	NA
All Japonica	1512	98.40%	1.10%	0.46%	0.07%	NA
Aus	269	64.30%	0.00%	11.52%	24.16%	NA
Indica I	595	22.90%	0.80%	11.43%	64.87%	NA
Indica II	465	77.60%	19.80%	0.65%	1.94%	NA
Indica III	913	81.30%	16.90%	0.55%	1.31%	NA
Indica Intermediate	786	75.30%	9.50%	2.67%	12.47%	NA
Temperate Japonica	767	99.60%	0.40%	0.00%	0.00%	NA
Tropical Japonica	504	96.80%	2.60%	0.60%	0.00%	NA
Japonica Intermediate	241	97.90%	0.00%	1.66%	0.41%	NA
VI/Aromatic	96	99.00%	0.00%	1.04%	0.00%	NA
Intermediate	90	86.70%	4.40%	4.44%	4.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1102378145	G -> A	LOC_Os11g05350.1	upstream_gene_variant ; 1663.0bp to feature; MODIFIER	silent_mutation	Average:58.595; most accessible tissue: Zhenshan97 root, score: 86.579	N	N	N	N
vg1102378145	G -> A	LOC_Os11g05360.1	upstream_gene_variant ; 994.0bp to feature; MODIFIER	silent_mutation	Average:58.595; most accessible tissue: Zhenshan97 root, score: 86.579	N	N	N	N
vg1102378145	G -> A	LOC_Os11g05370.1	downstream_gene_variant ; 4039.0bp to feature; MODIFIER	silent_mutation	Average:58.595; most accessible tissue: Zhenshan97 root, score: 86.579	N	N	N	N
vg1102378145	G -> A	LOC_Os11g05350-LOC_Os11g05360	intergenic_region ; MODIFIER	silent_mutation	Average:58.595; most accessible tissue: Zhenshan97 root, score: 86.579	N	N	N	N
vg1102378145	G -> DEL	N	N	silent_mutation	Average:58.595; most accessible tissue: Zhenshan97 root, score: 86.579	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1102378145	NA	2.97E-06	mr1598	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
vg1102378145	4.52E-06	NA	mr1611	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
vg1102378145	NA	2.21E-06	mr1842_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
vg1102378145	NA	1.07E-06	mr1933_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