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Detailed information for vg0208995135:

Variant ID: vg0208995135 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 8995135
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 103. )

Flanking Sequence (100 bp) in Reference Genome:

CCGGCAAGATCAACAACCCACGGAGAGGTGTATCGATCGCTAAGGCGCAACACAACGTCTTGTACGGTTGTAGTCGGATCACCAACGTTTCTCTCAAATC[G/A]
TAGTTACCTACAACTCACCGAAAGATCGGGCCAACAACAGCCTTGAGTGTCGAGAGGAACTTAGGGTTCATCAACTGAGGATGCCCCGTATCTAGACCAA

Reverse complement sequence

TTGGTCTAGATACGGGGCATCCTCAGTTGATGAACCCTAAGTTCCTCTCGACACTCAAGGCTGTTGTTGGCCCGATCTTTCGGTGAGTTGTAGGTAACTA[C/T]
GATTTGAGAGAAACGTTGGTGATCCGACTACAACCGTACAAGACGTTGTGTTGCGCCTTAGCGATCGATACACCTCTCCGTGGGTTGTTGATCTTGCCGG

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	96.70%	2.60%	0.72%	0.00%	NA
All Indica	2759	94.60%	4.20%	1.12%	0.00%	NA
All Japonica	1512	99.40%	0.40%	0.20%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	86.20%	11.10%	2.69%	0.00%	NA
Indica II	465	96.60%	1.90%	1.51%	0.00%	NA
Indica III	913	99.90%	0.10%	0.00%	0.00%	NA
Indica Intermediate	786	93.80%	5.20%	1.02%	0.00%	NA
Temperate Japonica	767	99.20%	0.70%	0.13%	0.00%	NA
Tropical Japonica	504	99.80%	0.00%	0.20%	0.00%	NA
Japonica Intermediate	241	99.20%	0.40%	0.41%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	100.00%	0.00%	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
vg0208995135	G -> A	LOC_Os02g15890.1	upstream_gene_variant ; 687.0bp to feature; MODIFIER	silent_mutation	Average:62.444; most accessible tissue: Zhenshan97 panicle, score: 77.482	N	N	N	N
vg0208995135	G -> A	LOC_Os02g15890-LOC_Os02g15900	intergenic_region ; MODIFIER	silent_mutation	Average:62.444; most accessible tissue: Zhenshan97 panicle, score: 77.482	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0208995135	4.11E-08	3.91E-09	mr1172_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