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Detailed information for vg0118245978:

Variant ID: vg0118245978 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 18245978
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: 281. )

Flanking Sequence (100 bp) in Reference Genome:

GACCGTCTTAGCCTTAGATAGATTGCACACGTTCCCTGAGTTCGATATCCTTTTGGGGTCACCCGAAGGTGAAGTGCTACAGCGGTATTCCGTGCGCTTG[C/T]
GGATTTCCTTTCCTTGATGGAGCAACCCATGATTCAAAACCTTTCTGCTCCTCGGGTTGATATTTGTGAGCCGTCCTGTTCTTCAAAACCAATCCTTTCA

Reverse complement sequence

TGAAAGGATTGGTTTTGAAGAACAGGACGGCTCACAAATATCAACCCGAGGAGCAGAAAGGTTTTGAATCATGGGTTGCTCCATCAAGGAAAGGAAATCC[G/A]
CAAGCGCACGGAATACCGCTGTAGCACTTCACCTTCGGGTGACCCCAAAAGGATATCGAACTCAGGGAACGTGTGCAATCTATCTAAGGCTAAGACGGTC

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	88.60%	0.60%	2.31%	8.55%	NA
All Indica	2759	81.50%	0.40%	3.81%	14.35%	NA
All Japonica	1512	98.70%	1.00%	0.13%	0.13%	NA
Aus	269	99.60%	0.40%	0.00%	0.00%	NA
Indica I	595	59.70%	0.50%	4.87%	34.96%	NA
Indica II	465	75.90%	0.40%	7.96%	15.70%	NA
Indica III	913	98.20%	0.00%	0.22%	1.53%	NA
Indica Intermediate	786	81.80%	0.60%	4.71%	12.85%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	99.00%	0.40%	0.40%	0.20%	NA
Japonica Intermediate	241	94.20%	5.40%	0.00%	0.41%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	90.00%	1.10%	2.22%	6.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0118245978	C -> T	LOC_Os01g33136.1	upstream_gene_variant ; 258.0bp to feature; MODIFIER	silent_mutation	Average:59.877; most accessible tissue: Zhenshan97 flag leaf, score: 77.738	N	N	N	N
vg0118245978	C -> T	LOC_Os01g33142.1	downstream_gene_variant ; 734.0bp to feature; MODIFIER	silent_mutation	Average:59.877; most accessible tissue: Zhenshan97 flag leaf, score: 77.738	N	N	N	N
vg0118245978	C -> T	LOC_Os01g33136-LOC_Os01g33142	intergenic_region ; MODIFIER	silent_mutation	Average:59.877; most accessible tissue: Zhenshan97 flag leaf, score: 77.738	N	N	N	N
vg0118245978	C -> DEL	N	N	silent_mutation	Average:59.877; most accessible tissue: Zhenshan97 flag leaf, score: 77.738	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0118245978	2.46E-06	1.20E-07	mr1236	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
vg0118245978	NA	1.07E-06	mr1236	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