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Detailed information for vg0228080556:

Variant ID: vg0228080556 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 28080556
Reference Allele: G	Alternative Allele: T
Primary Allele: T	Secondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.89, T: 0.12, others allele: 0.00, population size: 268. )

Flanking Sequence (100 bp) in Reference Genome:

TTCTCCGAACAAGTGTCAAGAAACCTTCTTCGGTAGCAGAAAATGCCCCTCGAACAACTTCCTCCGATACTGTTTCACTTTCTCGGGCAAGTCCTAGAAA[G/T]
ATAGGAAAGGTTGAGCAGTCATTTTGGTGCACTGAACAATTTCGGTTGAGATATGCTTGCCATTTATTAACGACAAGGATAAGGTCACATCATGCAGTCA

Reverse complement sequence

TGACTGCATGATGTGACCTTATCCTTGTCGTTAATAAATGGCAAGCATATCTCAACCGAAATTGTTCAGTGCACCAAAATGACTGCTCAACCTTTCCTAT[C/A]
TTTCTAGGACTTGCCCGAGAAAGTGAAACAGTATCGGAGGAAGTTGTTCGAGGGGCATTTTCTGCTACCGAAGAAGGTTTCTTGACACTTGTTCGGAGAA

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	58.60%	41.30%	0.13%	0.00%	NA
All Indica	2759	93.50%	6.30%	0.18%	0.00%	NA
All Japonica	1512	0.60%	99.40%	0.00%	0.00%	NA
Aus	269	55.80%	43.90%	0.37%	0.00%	NA
Indica I	595	97.30%	2.40%	0.34%	0.00%	NA
Indica II	465	97.40%	2.40%	0.22%	0.00%	NA
Indica III	913	88.60%	11.30%	0.11%	0.00%	NA
Indica Intermediate	786	93.90%	6.00%	0.13%	0.00%	NA
Temperate Japonica	767	0.30%	99.70%	0.00%	0.00%	NA
Tropical Japonica	504	1.20%	98.80%	0.00%	0.00%	NA
Japonica Intermediate	241	0.40%	99.60%	0.00%	0.00%	NA
VI/Aromatic	96	1.00%	99.00%	0.00%	0.00%	NA
Intermediate	90	34.40%	65.60%	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
vg0228080556	G -> T	LOC_Os02g46080.1	splice_region_variant&intron_variant ; LOW	silent_mutation	Average:65.346; most accessible tissue: Callus, score: 89.557	N	N	N	N
vg0228080556	G -> T	LOC_Os02g46080.2	splice_region_variant&intron_variant ; LOW	silent_mutation	Average:65.346; most accessible tissue: Callus, score: 89.557	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0228080556	NA	9.08E-09	mr1342	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
vg0228080556	NA	1.88E-77	mr1629	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