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Detailed information for vg0522891091:

Variant ID: vg0522891091 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 22891091
Reference Allele: T	Alternative Allele: G
Primary Allele: T	Secondary Allele: G

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.01, others allele: 0.00, population size: 236. )

Flanking Sequence (100 bp) in Reference Genome:

AAGGACCTCATCCTCCCCAGAAGCGTCCGCAACCCACATTAAAGAGTACCACCTGTTAGAGATAGGCCGAAAGATGATTGATAAAAGAGATTGGCAAAGA[T/G]
GTTCTCTAGCAGGAAAGAAGTAGGCCGAAAGGTGATTGATAAAGGATAAACAAAAACATGCTCTGCATCGCTCAAGGAAGACCCCTGATAGTAATTGCCC

Reverse complement sequence

GGGCAATTACTATCAGGGGTCTTCCTTGAGCGATGCAGAGCATGTTTTTGTTTATCCTTTATCAATCACCTTTCGGCCTACTTCTTTCCTGCTAGAGAAC[A/C]
TCTTTGCCAATCTCTTTTATCAATCATCTTTCGGCCTATCTCTAACAGGTGGTACTCTTTAATGTGGGTTGCGGACGCTTCTGGGGAGGATGAGGTCCTT

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	97.30%	1.00%	1.46%	0.32%	NA
All Indica	2759	95.60%	1.60%	2.32%	0.54%	NA
All Japonica	1512	100.00%	0.00%	0.00%	0.00%	NA
Aus	269	99.60%	0.00%	0.37%	0.00%	NA
Indica I	595	93.30%	2.70%	3.36%	0.67%	NA
Indica II	465	96.10%	1.10%	2.58%	0.22%	NA
Indica III	913	96.20%	1.00%	2.19%	0.66%	NA
Indica Intermediate	786	96.30%	1.70%	1.53%	0.51%	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	93.30%	2.20%	4.44%	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
vg0522891091	T -> DEL	N	N	silent_mutation	Average:15.698; most accessible tissue: Zhenshan97 flag leaf, score: 23.298	N	N	N	N
vg0522891091	T -> G	LOC_Os05g39020.1	upstream_gene_variant ; 2605.0bp to feature; MODIFIER	silent_mutation	Average:15.698; most accessible tissue: Zhenshan97 flag leaf, score: 23.298	N	N	N	N
vg0522891091	T -> G	LOC_Os05g39010.1	downstream_gene_variant ; 4295.0bp to feature; MODIFIER	silent_mutation	Average:15.698; most accessible tissue: Zhenshan97 flag leaf, score: 23.298	N	N	N	N
vg0522891091	T -> G	LOC_Os05g39030.1	downstream_gene_variant ; 611.0bp to feature; MODIFIER	silent_mutation	Average:15.698; most accessible tissue: Zhenshan97 flag leaf, score: 23.298	N	N	N	N
vg0522891091	T -> G	LOC_Os05g39030-LOC_Os05g39040	intergenic_region ; MODIFIER	silent_mutation	Average:15.698; most accessible tissue: Zhenshan97 flag leaf, score: 23.298	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0522891091	8.44E-07	NA	mr1829	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