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Detailed information for vg0827146562:

Variant ID: vg0827146562 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 27146562
Reference Allele: T	Alternative Allele: A
Primary Allele: A	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AACCAAATTACCATATGACCACATGCATATCAATAACTATTACCACTTAGTAATCTACTAATTAAAACCAAGGAAATTAATTGTTTTAGATTGCCTAATC[T/A]
TAATGTCTACTACCTAATTGTATGGCAAGGGGCACATGCCCCCCTTCCCAAAAAAAAAACTAACACACAACTTTATACATAATTAATAGTACGATATCCT

Reverse complement sequence

AGGATATCGTACTATTAATTATGTATAAAGTTGTGTGTTAGTTTTTTTTTTGGGAAGGGGGGCATGTGCCCCTTGCCATACAATTAGGTAGTAGACATTA[A/T]
GATTAGGCAATCTAAAACAATTAATTTCCTTGGTTTTAATTAGTAGATTACTAAGTGGTAATAGTTATTGATATGCATGTGGTCATATGGTAATTTGGTT

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	90.60%	7.80%	1.63%	0.00%	NA
All Indica	2759	99.80%	0.00%	0.18%	0.00%	NA
All Japonica	1512	71.80%	23.80%	4.43%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	99.80%	0.00%	0.22%	0.00%	NA
Indica III	913	99.90%	0.00%	0.11%	0.00%	NA
Indica Intermediate	786	99.60%	0.00%	0.38%	0.00%	NA
Temperate Japonica	767	50.50%	42.40%	7.17%	0.00%	NA
Tropical Japonica	504	94.60%	3.80%	1.59%	0.00%	NA
Japonica Intermediate	241	91.70%	6.60%	1.66%	0.00%	NA
VI/Aromatic	96	99.00%	0.00%	1.04%	0.00%	NA
Intermediate	90	85.60%	10.00%	4.44%	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
vg0827146562	T -> A	LOC_Os08g42950.1	downstream_gene_variant ; 1593.0bp to feature; MODIFIER	silent_mutation	Average:37.671; most accessible tissue: Callus, score: 82.251	N	N	N	N
vg0827146562	T -> A	LOC_Os08g42950-LOC_Os08g42960	intergenic_region ; MODIFIER	silent_mutation	Average:37.671; most accessible tissue: Callus, score: 82.251	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0827146562	NA	1.31E-06	mr1163	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
vg0827146562	NA	9.40E-10	mr1002_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
vg0827146562	NA	7.50E-08	mr1010_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
vg0827146562	NA	4.17E-11	mr1011_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
vg0827146562	NA	9.35E-11	mr1576_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
vg0827146562	NA	1.09E-07	mr1576_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
vg0827146562	1.06E-07	NA	mr1712_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
vg0827146562	1.58E-06	NA	mr1717_2	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
vg0827146562	7.57E-06	NA	mr1768_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
vg0827146562	NA	2.61E-07	mr1768_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
vg0827146562	NA	5.22E-09	mr1946_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
vg0827146562	NA	5.22E-09	mr1948_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
vg0827146562	5.08E-07	3.26E-10	mr1977_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
vg0827146562	NA	5.77E-07	mr1977_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