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Detailed information for vg1017458025:

Variant ID: vg1017458025 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 17458025
Reference Allele: G	Alternative Allele: A
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.96, A: 0.04, others allele: 0.00, population size: 109. )

Flanking Sequence (100 bp) in Reference Genome:

GATTCCCAGCTCGTCACCGCCCCAAGGGCCGTCGTCGGAGACCTCTGGAACCGCTGTCGAGGAAAATCAATCTCTTCCACCGGACTCCCAGGCATCTGCC[G/A]
CCCCTAGGGCAGCCACCGTCAACGGGATCCGCCTCCTCACTGCGAACCTTGAACTGGCACTCAGGCTGCCACCGTCTCGGTTGGACGCTGCCCCTAGGGC

Reverse complement sequence

GCCCTAGGGGCAGCGTCCAACCGAGACGGTGGCAGCCTGAGTGCCAGTTCAAGGTTCGCAGTGAGGAGGCGGATCCCGTTGACGGTGGCTGCCCTAGGGG[C/T]
GGCAGATGCCTGGGAGTCCGGTGGAAGAGATTGATTTTCCTCGACAGCGGTTCCAGAGGTCTCCGACGACGGCCCTTGGGGCGGTGACGAGCTGGGAATC

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	58.00%	41.70%	0.06%	0.25%	NA
All Indica	2759	91.20%	8.40%	0.07%	0.33%	NA
All Japonica	1512	8.10%	91.90%	0.00%	0.00%	NA
Aus	269	12.60%	86.60%	0.00%	0.74%	NA
Indica I	595	95.60%	3.70%	0.17%	0.50%	NA
Indica II	465	92.50%	7.10%	0.22%	0.22%	NA
Indica III	913	88.60%	11.30%	0.00%	0.11%	NA
Indica Intermediate	786	90.10%	9.40%	0.00%	0.51%	NA
Temperate Japonica	767	2.00%	98.00%	0.00%	0.00%	NA
Tropical Japonica	504	4.80%	95.20%	0.00%	0.00%	NA
Japonica Intermediate	241	34.40%	65.60%	0.00%	0.00%	NA
VI/Aromatic	96	24.00%	76.00%	0.00%	0.00%	NA
Intermediate	90	52.20%	45.60%	1.11%	1.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1017458025	G -> A	LOC_Os10g33260.1	missense_variant ; p.Ala62Thr; MODERATE	nonsynonymous_codon ; A62T	Average:71.97; most accessible tissue: Zhenshan97 panicle, score: 87.764	unknown	unknown	DELETERIOUS	0.00
vg1017458025	G -> DEL	LOC_Os10g33260.1	N	frameshift_variant	Average:71.97; most accessible tissue: Zhenshan97 panicle, score: 87.764	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1017458025	NA	9.19E-24	mr1020	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
vg1017458025	NA	3.03E-19	mr1021	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
vg1017458025	NA	4.33E-14	mr1032	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
vg1017458025	NA	5.06E-09	mr1047	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
vg1017458025	NA	6.99E-15	mr1165	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
vg1017458025	NA	1.36E-41	mr1200	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
vg1017458025	NA	7.32E-10	mr1524	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
vg1017458025	NA	2.60E-07	mr1716	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
vg1017458025	NA	3.82E-06	mr1782	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
vg1017458025	NA	1.18E-06	mr1796	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
vg1017458025	NA	6.91E-22	mr1971	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
vg1017458025	NA	1.11E-06	mr1990	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
vg1017458025	NA	4.96E-10	mr1782_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