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Detailed information for vg1006597026:

Variant ID: vg1006597026 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 6597026
Reference Allele: C	Alternative Allele: T
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.98, T: 0.02, others allele: 0.00, population size: 90. )

Flanking Sequence (100 bp) in Reference Genome:

ACTGACATGTGGGTCCCACGTCTATTGGTCTGATGGAAAACAAGACGGAGTGGCTGTGGGGGTACCCGGTTTGAGTACGGTATCCCGAAACCACCCGCGA[C/T]
CGTTCAGGATTTCGATCGCGCACAAATTGATAAACAGAACAGCTTTCGATATATATACCCAAGTTTTTACAGAAATTATTACATAAAAGATAACTAAGAC

Reverse complement sequence

GTCTTAGTTATCTTTTATGTAATAATTTCTGTAAAAACTTGGGTATATATATCGAAAGCTGTTCTGTTTATCAATTTGTGCGCGATCGAAATCCTGAACG[G/A]
TCGCGGGTGGTTTCGGGATACCGTACTCAAACCGGGTACCCCCACAGCCACTCCGTCTTGTTTTCCATCAGACCAATAGACGTGGGACCCACATGTCAGT

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	21.90%	19.40%	13.03%	45.60%	NA
All Indica	2759	36.10%	1.30%	21.64%	40.92%	NA
All Japonica	1512	1.00%	56.50%	0.53%	42.00%	NA
Aus	269	1.10%	0.40%	1.12%	97.40%	NA
Indica I	595	9.90%	1.70%	23.70%	64.71%	NA
Indica II	465	60.20%	0.60%	12.47%	26.67%	NA
Indica III	913	36.50%	0.90%	27.16%	35.49%	NA
Indica Intermediate	786	41.30%	1.90%	19.08%	37.66%	NA
Temperate Japonica	767	0.40%	88.70%	0.13%	10.82%	NA
Tropical Japonica	504	0.80%	8.30%	0.40%	90.48%	NA
Japonica Intermediate	241	3.30%	54.80%	2.07%	39.83%	NA
VI/Aromatic	96	3.10%	5.20%	0.00%	91.67%	NA
Intermediate	90	20.00%	25.60%	8.89%	45.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1006597026	C -> T	LOC_Os10g11889.1	downstream_gene_variant ; 27.0bp to feature; MODIFIER	silent_mutation	Average:23.458; most accessible tissue: Callus, score: 57.04	N	N	N	N
vg1006597026	C -> T	LOC_Os10g11889.2	downstream_gene_variant ; 27.0bp to feature; MODIFIER	silent_mutation	Average:23.458; most accessible tissue: Callus, score: 57.04	N	N	N	N
vg1006597026	C -> T	LOC_Os10g11870-LOC_Os10g11889	intergenic_region ; MODIFIER	silent_mutation	Average:23.458; most accessible tissue: Callus, score: 57.04	N	N	N	N
vg1006597026	C -> DEL	N	N	silent_mutation	Average:23.458; most accessible tissue: Callus, score: 57.04	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1006597026	NA	4.15E-07	mr1304	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
vg1006597026	8.79E-07	1.08E-07	mr1414	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
vg1006597026	4.92E-06	4.92E-06	mr1424	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
vg1006597026	NA	8.90E-10	mr1709	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
vg1006597026	NA	1.86E-08	mr1709	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
vg1006597026	NA	9.85E-07	mr1027_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