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Detailed information for vg0421395712:

Variant ID: vg0421395712 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 21395712
Reference Allele: A	Alternative Allele: T
Primary Allele: A	Secondary Allele: T

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 340. )

Flanking Sequence (100 bp) in Reference Genome:

ATATTCATCACCTAAACAAATGTGAAAGAAGTAAATAATAAAGAATCTCTCCCCCAAGTAGCTAGCAACACATTTTTGTATGCACCTGTAGCACAGTACT[A/T]
GTAGTTATTACTATTGTTTATCGTCTTTAATTAGCGCAAAAAAACAAAGAAAGATGTGCAGTTGTATTGCTGAAGAAAACATGCATGCATCGATCTTGAG

Reverse complement sequence

CTCAAGATCGATGCATGCATGTTTTCTTCAGCAATACAACTGCACATCTTTCTTTGTTTTTTTGCGCTAATTAAAGACGATAAACAATAGTAATAACTAC[T/A]
AGTACTGTGCTACAGGTGCATACAAAAATGTGTTGCTAGCTACTTGGGGGAGAGATTCTTTATTATTTACTTCTTTCACATTTGTTTAGGTGATGAATAT

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	84.60%	1.10%	2.39%	11.91%	NA
All Indica	2759	78.50%	0.00%	3.33%	18.16%	NA
All Japonica	1512	95.20%	3.20%	0.79%	0.86%	NA
Aus	269	96.70%	0.00%	1.49%	1.86%	NA
Indica I	595	84.00%	0.00%	2.02%	13.95%	NA
Indica II	465	80.20%	0.20%	4.95%	14.62%	NA
Indica III	913	73.10%	0.00%	4.49%	22.45%	NA
Indica Intermediate	786	79.50%	0.00%	2.04%	18.45%	NA
Temperate Japonica	767	92.20%	6.30%	1.56%	0.00%	NA
Tropical Japonica	504	97.40%	0.00%	0.00%	2.58%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	60.40%	0.00%	3.12%	36.46%	NA
Intermediate	90	84.40%	3.30%	2.22%	10.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0421395712	A -> DEL	N	N	silent_mutation	Average:51.804; most accessible tissue: Callus, score: 83.757	N	N	N	N
vg0421395712	A -> T	LOC_Os04g35210.1	upstream_gene_variant ; 1069.0bp to feature; MODIFIER	silent_mutation	Average:51.804; most accessible tissue: Callus, score: 83.757	N	N	N	N
vg0421395712	A -> T	LOC_Os04g35200-LOC_Os04g35210	intergenic_region ; MODIFIER	silent_mutation	Average:51.804; most accessible tissue: Callus, score: 83.757	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0421395712	7.69E-06	7.69E-06	mr1234_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
vg0421395712	1.06E-06	1.06E-06	mr1828_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