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Detailed information for vg0110745222:

Variant ID: vg0110745222 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 10745222
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, others allele: 0.00, population size: 122. )

Flanking Sequence (100 bp) in Reference Genome:

GTGCGACCACATGGGTGGAATGGGACACCCCTGGCTGAGTAACTAGCTAATCGGAGGAACCATGATGCCAAGAGACATGTGGATTCAACGGGGTGGTGCC[G/A]
GGGAGAACCCCCGGGCTTCCTGGCACAGTATGGTCTGGGACCTAACCTGATGTCGGTCTGGGACCCCTCTCGTTGGCATATGGTGAACCTGTGTCGGCTT

Reverse complement sequence

AAGCCGACACAGGTTCACCATATGCCAACGAGAGGGGTCCCAGACCGACATCAGGTTAGGTCCCAGACCATACTGTGCCAGGAAGCCCGGGGGTTCTCCC[C/T]
GGCACCACCCCGTTGAATCCACATGTCTCTTGGCATCATGGTTCCTCCGATTAGCTAGTTACTCAGCCAGGGGTGTCCCATTCCACCCATGTGGTCGCAC

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	91.90%	4.30%	3.79%	0.00%	NA
All Indica	2759	86.20%	7.40%	6.38%	0.00%	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	75.60%	13.80%	10.59%	0.00%	NA
Indica II	465	94.80%	2.20%	3.01%	0.00%	NA
Indica III	913	90.80%	5.10%	4.05%	0.00%	NA
Indica Intermediate	786	83.70%	8.40%	7.89%	0.00%	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	96.70%	0.00%	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
vg0110745222	G -> A	LOC_Os01g19010.1	upstream_gene_variant ; 1745.0bp to feature; MODIFIER	silent_mutation	Average:40.141; most accessible tissue: Minghui63 root, score: 58.187	N	N	N	N
vg0110745222	G -> A	LOC_Os01g19020.1	downstream_gene_variant ; 3381.0bp to feature; MODIFIER	silent_mutation	Average:40.141; most accessible tissue: Minghui63 root, score: 58.187	N	N	N	N
vg0110745222	G -> A	LOC_Os01g19010-LOC_Os01g19020	intergenic_region ; MODIFIER	silent_mutation	Average:40.141; most accessible tissue: Minghui63 root, score: 58.187	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0110745222	3.11E-06	NA	mr1125	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