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Detailed information for vg0517742966:

Variant ID: vg0517742966 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 17742966
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 74. )

Flanking Sequence (100 bp) in Reference Genome:

CATCATGGCCGCCGATCAGATCCTCGCGCAGCCTTGGTGGGTTGGCTCACGAACATGGCGGTTTGGCCTAGCTGAGACGATGGTGCTGCTATTTCCACTG[C/T]
CAACATCGTCGGCTGATGGAAAAGAGAGGAGAGAGGAAGATAGTGAGGGGAAAAGAGGAGAGTCATTGATATATAGGACCCACATTTTATGTTAGCAAAC

Reverse complement sequence

GTTTGCTAACATAAAATGTGGGTCCTATATATCAATGACTCTCCTCTTTTCCCCTCACTATCTTCCTCTCTCCTCTCTTTTCCATCAGCCGACGATGTTG[G/A]
CAGTGGAAATAGCAGCACCATCGTCTCAGCTAGGCCAAACCGCCATGTTCGTGAGCCAACCCACCAAGGCTGCGCGAGGATCTGATCGGCGGCCATGATG

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	38.00%	15.70%	2.22%	44.05%	NA
All Indica	2759	10.00%	23.30%	3.37%	63.36%	NA
All Japonica	1512	91.30%	2.40%	0.07%	6.28%	NA
Aus	269	3.70%	19.30%	3.35%	73.61%	NA
Indica I	595	8.10%	32.30%	5.71%	53.95%	NA
Indica II	465	31.40%	17.00%	2.80%	48.82%	NA
Indica III	913	2.10%	18.90%	1.64%	77.33%	NA
Indica Intermediate	786	8.00%	25.20%	3.94%	62.85%	NA
Temperate Japonica	767	97.30%	0.50%	0.00%	2.22%	NA
Tropical Japonica	504	79.20%	5.80%	0.20%	14.88%	NA
Japonica Intermediate	241	97.50%	1.20%	0.00%	1.24%	NA
VI/Aromatic	96	88.50%	5.20%	0.00%	6.25%	NA
Intermediate	90	52.20%	6.70%	2.22%	38.89%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0517742966	C -> T	LOC_Os05g30630.1	upstream_gene_variant ; 135.0bp to feature; MODIFIER	silent_mutation	Average:64.532; most accessible tissue: Callus, score: 95.885	N	N	N	N
vg0517742966	C -> T	LOC_Os05g30620.1	downstream_gene_variant ; 4448.0bp to feature; MODIFIER	silent_mutation	Average:64.532; most accessible tissue: Callus, score: 95.885	N	N	N	N
vg0517742966	C -> T	LOC_Os05g30630-LOC_Os05g30640	intergenic_region ; MODIFIER	silent_mutation	Average:64.532; most accessible tissue: Callus, score: 95.885	N	N	N	N
vg0517742966	C -> DEL	N	N	silent_mutation	Average:64.532; most accessible tissue: Callus, score: 95.885	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0517742966	6.63E-07	6.63E-07	mr1827	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
vg0517742966	NA	1.30E-08	mr1399_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
vg0517742966	4.40E-07	1.09E-08	mr1399_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
vg0517742966	NA	7.15E-06	mr1827_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