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Detailed information for vg0105661905:

Variant ID: vg0105661905 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 5661905
Reference Allele: T	Alternative Allele: G
Primary Allele: T	Secondary Allele: G

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.99, others allele: 0.00, population size: 268. )

Flanking Sequence (100 bp) in Reference Genome:

TTCAAATTATGTCTGATCTTTATTTTTCTAATTTAGCCTCAGATAACTTTTTTTGCACACTGCGCAAGTTCTAATTCATAATTACAAGTGGCTACAGCAC[T/G]
GACATCTCACTGTATGTACATCGATCTCAATTGAAGGTGATTTTGTTTTTGTTTTCTTTGAGATCAACTGTATGTATAATTCTGAATGTGCCTTTTTTGG

Reverse complement sequence

CCAAAAAAGGCACATTCAGAATTATACATACAGTTGATCTCAAAGAAAACAAAAACAAAATCACCTTCAATTGAGATCGATGTACATACAGTGAGATGTC[A/C]
GTGCTGTAGCCACTTGTAATTATGAATTAGAACTTGCGCAGTGTGCAAAAAAAGTTATCTGAGGCTAAATTAGAAAAATAAAGATCAGACATAATTTGAA

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	67.90%	31.70%	0.47%	0.00%	NA
All Indica	2759	79.90%	19.90%	0.18%	0.00%	NA
All Japonica	1512	43.90%	55.20%	0.93%	0.00%	NA
Aus	269	95.20%	4.80%	0.00%	0.00%	NA
Indica I	595	57.50%	42.20%	0.34%	0.00%	NA
Indica II	465	77.80%	22.20%	0.00%	0.00%	NA
Indica III	913	96.60%	3.30%	0.11%	0.00%	NA
Indica Intermediate	786	78.80%	21.00%	0.25%	0.00%	NA
Temperate Japonica	767	60.40%	37.90%	1.69%	0.00%	NA
Tropical Japonica	504	21.60%	78.40%	0.00%	0.00%	NA
Japonica Intermediate	241	38.20%	61.40%	0.41%	0.00%	NA
VI/Aromatic	96	24.00%	75.00%	1.04%	0.00%	NA
Intermediate	90	65.60%	32.20%	2.22%	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
vg0105661905	T -> G	LOC_Os01g10600.1	downstream_gene_variant ; 1418.0bp to feature; MODIFIER	silent_mutation	Average:40.406; most accessible tissue: Callus, score: 61.709	N	N	N	N
vg0105661905	T -> G	LOC_Os01g10590-LOC_Os01g10600	intergenic_region ; MODIFIER	silent_mutation	Average:40.406; most accessible tissue: Callus, score: 61.709	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0105661905	1.62E-09	1.65E-15	mr1498	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
vg0105661905	3.66E-12	1.29E-20	mr1498	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
vg0105661905	1.16E-08	1.52E-12	mr1769	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
vg0105661905	NA	6.29E-07	mr1795	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
vg0105661905	NA	2.03E-10	mr1925	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
vg0105661905	1.42E-07	3.70E-15	mr1925	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
vg0105661905	NA	1.62E-10	mr1951	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
vg0105661905	6.52E-09	2.66E-14	mr1951	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
vg0105661905	NA	3.78E-06	mr1236_2	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
vg0105661905	6.10E-08	1.58E-16	mr1498_2	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
vg0105661905	2.40E-10	4.48E-19	mr1498_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
vg0105661905	NA	2.31E-11	mr1769_2	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
vg0105661905	2.87E-09	3.60E-16	mr1769_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
vg0105661905	NA	2.20E-06	mr1795_2	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
vg0105661905	1.66E-07	6.42E-11	mr1925_2	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
vg0105661905	3.67E-08	1.05E-15	mr1925_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
vg0105661905	NA	5.72E-10	mr1951_2	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
vg0105661905	8.85E-07	2.51E-14	mr1951_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
vg0105661905	NA	3.25E-07	mr1959_2	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