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Detailed information for vg0206158957:

Variant ID: vg0206158957 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 6158957
Reference Allele: G	Alternative Allele: T
Primary Allele: T	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GTTTTTCATCGTTTTCTTATTGGTTTATCAGTTATCACGGTCAGGTTTAATGTTTCGGATATTAATTTCAATAATTTTAGAGATTATTGTCCTATAGTCC[G/T]
CGATAGGACATTATGATCTCTGAAATATTTATTTTTTTAATCAAGCATTTTTGAAGTTCAACATAAATTTGTTAAAGCTTTAACTTGTTTGATTCCGAAA

Reverse complement sequence

TTTCGGAATCAAACAAGTTAAAGCTTTAACAAATTTATGTTGAACTTCAAAAATGCTTGATTAAAAAAATAAATATTTCAGAGATCATAATGTCCTATCG[C/A]
GGACTATAGGACAATAATCTCTAAAATTATTGAAATTAATATCCGAAACATTAAACCTGACCGTGATAACTGATAAACCAATAAGAAAACGATGAAAAAC

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	56.50%	31.10%	0.13%	12.19%	NA
All Indica	2759	81.60%	0.80%	0.18%	17.47%	NA
All Japonica	1512	3.20%	92.00%	0.07%	4.70%	NA
Aus	269	98.90%	0.40%	0.00%	0.74%	NA
Indica I	595	74.50%	0.20%	0.34%	25.04%	NA
Indica II	465	79.80%	0.60%	0.00%	19.57%	NA
Indica III	913	84.60%	0.40%	0.22%	14.79%	NA
Indica Intermediate	786	84.50%	1.80%	0.13%	13.61%	NA
Temperate Japonica	767	2.60%	88.80%	0.13%	8.47%	NA
Tropical Japonica	504	3.40%	96.00%	0.00%	0.60%	NA
Japonica Intermediate	241	5.00%	93.80%	0.00%	1.24%	NA
VI/Aromatic	96	62.50%	20.80%	0.00%	16.67%	NA
Intermediate	90	52.20%	42.20%	0.00%	5.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0206158957	G -> T	LOC_Os02g11880.1	upstream_gene_variant ; 3802.0bp to feature; MODIFIER	silent_mutation	Average:53.377; most accessible tissue: Callus, score: 78.601	N	N	N	N
vg0206158957	G -> T	LOC_Os02g11900.1	downstream_gene_variant ; 4518.0bp to feature; MODIFIER	silent_mutation	Average:53.377; most accessible tissue: Callus, score: 78.601	N	N	N	N
vg0206158957	G -> T	LOC_Os02g11890.1	intron_variant ; MODIFIER	silent_mutation	Average:53.377; most accessible tissue: Callus, score: 78.601	N	N	N	N
vg0206158957	G -> DEL	N	N	silent_mutation	Average:53.377; most accessible tissue: Callus, score: 78.601	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0206158957	NA	9.94E-22	mr1122	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
vg0206158957	NA	5.85E-46	mr1136	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
vg0206158957	NA	2.22E-21	mr1168	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
vg0206158957	NA	3.99E-10	mr1175	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
vg0206158957	NA	1.72E-23	mr1383	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
vg0206158957	NA	3.58E-18	mr1557	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
vg0206158957	NA	8.24E-14	mr1653	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
vg0206158957	NA	1.20E-18	mr1715	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
vg0206158957	NA	1.86E-57	mr1136_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
vg0206158957	NA	7.38E-32	mr1137_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
vg0206158957	NA	4.04E-24	mr1383_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
vg0206158957	NA	1.87E-33	mr1448_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
vg0206158957	NA	3.89E-28	mr1617_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
vg0206158957	NA	3.50E-19	mr1637_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
vg0206158957	NA	4.23E-18	mr1945_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