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Detailed information for vg0801235869:

Variant ID: vg0801235869 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 1235869
Reference Allele: A	Alternative Allele: T
Primary Allele: A	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TACATGTGGTTCGGGGCCTATTTATACTCGAAAATTACAAACTATGTCCATATCGGACACGACTCTTATCTCTAACAAACTCTAAGATACCATAAGTCTT[A/T]
ACGGCAGACTTTTGCCCAAACATATATCTAAGGAAATTACATAAAATATCATAATTAATAGATACAATTGCCTTCCCAGGACTCTATCCACGCGTGGCCA

Reverse complement sequence

TGGCCACGCGTGGATAGAGTCCTGGGAAGGCAATTGTATCTATTAATTATGATATTTTATGTAATTTCCTTAGATATATGTTTGGGCAAAAGTCTGCCGT[T/A]
AAGACTTATGGTATCTTAGAGTTTGTTAGAGATAAGAGTCGTGTCCGATATGGACATAGTTTGTAATTTTCGAGTATAAATAGGCCCCGAACCACATGTA

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	36.50%	0.70%	0.91%	61.96%	NA
All Indica	2759	18.70%	0.90%	1.38%	79.09%	NA
All Japonica	1512	56.10%	0.10%	0.20%	43.65%	NA
Aus	269	87.40%	0.00%	0.00%	12.64%	NA
Indica I	595	5.90%	0.30%	0.67%	93.11%	NA
Indica II	465	7.10%	1.50%	1.29%	90.11%	NA
Indica III	913	28.10%	0.80%	2.30%	68.78%	NA
Indica Intermediate	786	24.20%	1.00%	0.89%	73.92%	NA
Temperate Japonica	767	68.70%	0.00%	0.26%	31.03%	NA
Tropical Japonica	504	24.60%	0.00%	0.20%	75.20%	NA
Japonica Intermediate	241	81.70%	0.40%	0.00%	17.84%	NA
VI/Aromatic	96	91.70%	3.10%	1.04%	4.17%	NA
Intermediate	90	42.20%	3.30%	1.11%	53.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0801235869	A -> T	LOC_Os08g02890.1	upstream_gene_variant ; 585.0bp to feature; MODIFIER	silent_mutation	Average:6.24; most accessible tissue: Zhenshan97 young leaf, score: 10.848	N	N	N	N
vg0801235869	A -> T	LOC_Os08g02900.1	downstream_gene_variant ; 2911.0bp to feature; MODIFIER	silent_mutation	Average:6.24; most accessible tissue: Zhenshan97 young leaf, score: 10.848	N	N	N	N
vg0801235869	A -> T	LOC_Os08g02880-LOC_Os08g02890	intergenic_region ; MODIFIER	silent_mutation	Average:6.24; most accessible tissue: Zhenshan97 young leaf, score: 10.848	N	N	N	N
vg0801235869	A -> DEL	N	N	silent_mutation	Average:6.24; most accessible tissue: Zhenshan97 young leaf, score: 10.848	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0801235869	NA	1.90E-06	mr1092	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
vg0801235869	NA	9.74E-06	mr1097	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