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Detailed information for vg0802994561:

Variant ID: vg0802994561 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 2994561
Reference Allele: T	Alternative Allele: G
Primary Allele: T	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AAAGCTAGCTTGCAGGTACTTCCTCTATCCACATTAGTTTTCCATATGATTCCAGGTACACGTGCGTAATTGAAGGTGTGTTCAAGTTAAAATATTTGAG[T/G]
TCAATTGTGAGTTTTGAGGTTATTTTTGTCTAGATTAACCCCACGGCAACAAAAGTCGACAACTGTGGTATTTTGTCAAAGAAATGAACACACATCTTAA

Reverse complement sequence

TTAAGATGTGTGTTCATTTCTTTGACAAAATACCACAGTTGTCGACTTTTGTTGCCGTGGGGTTAATCTAGACAAAAATAACCTCAAAACTCACAATTGA[A/C]
CTCAAATATTTTAACTTGAACACACCTTCAATTACGCACGTGTACCTGGAATCATATGGAAAACTAATGTGGATAGAGGAAGTACCTGCAAGCTAGCTTT

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	97.90%	1.80%	0.34%	0.00%	NA
All Indica	2759	99.80%	0.00%	0.18%	0.00%	NA
All Japonica	1512	93.70%	5.60%	0.73%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	99.80%	0.00%	0.17%	0.00%	NA
Indica II	465	99.60%	0.00%	0.43%	0.00%	NA
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	99.70%	0.00%	0.25%	0.00%	NA
Temperate Japonica	767	87.90%	10.70%	1.43%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	99.20%	0.80%	0.00%	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
vg0802994561	T -> G	LOC_Os08g05600.1	upstream_gene_variant ; 2470.0bp to feature; MODIFIER	silent_mutation	Average:43.805; most accessible tissue: Callus, score: 79.843	N	N	N	N
vg0802994561	T -> G	LOC_Os08g05590.1	downstream_gene_variant ; 3545.0bp to feature; MODIFIER	silent_mutation	Average:43.805; most accessible tissue: Callus, score: 79.843	N	N	N	N
vg0802994561	T -> G	LOC_Os08g05590-LOC_Os08g05600	intergenic_region ; MODIFIER	silent_mutation	Average:43.805; most accessible tissue: Callus, score: 79.843	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0802994561	NA	1.60E-09	mr1062	Jap_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
vg0802994561	2.79E-07	3.02E-11	mr1062_2	Jap_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
vg0802994561	NA	7.14E-06	mr1631_2	Jap_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