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Detailed information for vg0205394361:

Variant ID: vg0205394361 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 5394361
Reference Allele: T	Alternative Allele: A
Primary Allele: T	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TGTGGCACTTGATTGATCATCTCCACGCCGGGTCATTGCTTGTTACTCTTGGAGGTTGCCGCCTCCTAGACGGCTTGTGGAGGAGTTGTCCGGTGACCTC[T/A]
CCGAGAAAATTGTGGAGGAGGCCCGGCGCCGGTTTGTGAGTGGTTTGGAGTTCACCACCTTCGGAGTGAAGAAAGAACTACCCTAGTGATCGAGGCTTGG

Reverse complement sequence

CCAAGCCTCGATCACTAGGGTAGTTCTTTCTTCACTCCGAAGGTGGTGAACTCCAAACCACTCACAAACCGGCGCCGGGCCTCCTCCACAATTTTCTCGG[A/T]
GAGGTCACCGGACAACTCCTCCACAAGCCGTCTAGGAGGCGGCAACCTCCAAGAGTAACAAGCAATGACCCGGCGTGGAGATGATCAATCAAGTGCCACA

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	87.60%	0.70%	8.04%	3.72%	NA
All Indica	2759	79.80%	1.20%	13.05%	5.94%	NA
All Japonica	1512	99.60%	0.00%	0.07%	0.33%	NA
Aus	269	94.80%	0.00%	4.46%	0.74%	NA
Indica I	595	60.70%	3.90%	26.72%	8.74%	NA
Indica II	465	83.90%	0.60%	9.03%	6.45%	NA
Indica III	913	88.30%	0.10%	9.09%	2.52%	NA
Indica Intermediate	786	82.20%	0.60%	9.67%	7.51%	NA
Temperate Japonica	767	99.60%	0.00%	0.13%	0.26%	NA
Tropical Japonica	504	99.80%	0.00%	0.00%	0.20%	NA
Japonica Intermediate	241	99.20%	0.00%	0.00%	0.83%	NA
VI/Aromatic	96	99.00%	0.00%	1.04%	0.00%	NA
Intermediate	90	87.80%	0.00%	6.67%	5.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0205394361	T -> A	LOC_Os02g10270.1	downstream_gene_variant ; 1703.0bp to feature; MODIFIER	silent_mutation	Average:18.763; most accessible tissue: Zhenshan97 panicle, score: 39.652	N	N	N	N
vg0205394361	T -> A	LOC_Os02g10280.1	downstream_gene_variant ; 1882.0bp to feature; MODIFIER	silent_mutation	Average:18.763; most accessible tissue: Zhenshan97 panicle, score: 39.652	N	N	N	N
vg0205394361	T -> A	LOC_Os02g10270-LOC_Os02g10280	intergenic_region ; MODIFIER	silent_mutation	Average:18.763; most accessible tissue: Zhenshan97 panicle, score: 39.652	N	N	N	N
vg0205394361	T -> DEL	N	N	silent_mutation	Average:18.763; most accessible tissue: Zhenshan97 panicle, score: 39.652	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0205394361	3.48E-06	8.78E-06	mr1338_2	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
vg0205394361	NA	8.08E-07	mr1519_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
vg0205394361	NA	1.36E-06	mr1874_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