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Detailed information for vg0223848979:

Variant ID: vg0223848979 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 23848979
Reference Allele: A	Alternative Allele: T
Primary Allele: A	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CCCCTACCCCTTTGTACCCGCCCCCTAAACCTAATACCTAATTGGTCAAGGGCATCGTCGTTGTCAAGCTCGCAAGAGTGGAAGGAGAAGGTCACGGTGC[A/T]
CGAATCTCAGAGCCGATCAGAGCATCCAAATTTTGAAAGATGGGGTTTCGATTATGTCCAATGGAGGTTAGAAATTCTGATACTAGTTTTCATGCCATTG

Reverse complement sequence

CAATGGCATGAAAACTAGTATCAGAATTTCTAACCTCCATTGGACATAATCGAAACCCCATCTTTCAAAATTTGGATGCTCTGATCGGCTCTGAGATTCG[T/A]
GCACCGTGACCTTCTCCTTCCACTCTTGCGAGCTTGACAACGACGATGCCCTTGACCAATTAGGTATTAGGTTTAGGGGGCGGGTACAAAGGGGTAGGGG

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	98.20%	1.20%	0.63%	0.00%	NA
All Indica	2759	99.80%	0.00%	0.22%	0.00%	NA
All Japonica	1512	94.90%	3.50%	1.59%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	99.00%	0.00%	1.01%	0.00%	NA
Indica II	465	100.00%	0.00%	0.00%	0.00%	NA
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	100.00%	0.00%	0.00%	0.00%	NA
Temperate Japonica	767	90.10%	6.90%	3.00%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	99.60%	0.00%	0.41%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	97.80%	2.20%	0.00%	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
vg0223848979	A -> T	LOC_Os02g39520.1	upstream_gene_variant ; 760.0bp to feature; MODIFIER	silent_mutation	Average:67.323; most accessible tissue: Zhenshan97 young leaf, score: 82.077	N	N	N	N
vg0223848979	A -> T	LOC_Os02g39520.2	upstream_gene_variant ; 760.0bp to feature; MODIFIER	silent_mutation	Average:67.323; most accessible tissue: Zhenshan97 young leaf, score: 82.077	N	N	N	N
vg0223848979	A -> T	LOC_Os02g39510.1	downstream_gene_variant ; 2375.0bp to feature; MODIFIER	silent_mutation	Average:67.323; most accessible tissue: Zhenshan97 young leaf, score: 82.077	N	N	N	N
vg0223848979	A -> T	LOC_Os02g39510-LOC_Os02g39520	intergenic_region ; MODIFIER	silent_mutation	Average:67.323; most accessible tissue: Zhenshan97 young leaf, score: 82.077	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0223848979	1.57E-06	NA	mr1113	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