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Detailed information for vg0622854546:

Variant ID: vg0622854546 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 22854546
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.98, others allele: 0.00, population size: 68. )

Flanking Sequence (100 bp) in Reference Genome:

GGGTAGGATCTGGCCTAATGACCAGATCCAATGTTCTTCTAATGAGAAAGGAGAGGAGCGGATGAAAGGCTCGTTGGAGATGTCGGCAATGGTTAGGGAA[C/T]
GATTTTGAATCTAGGGCATAAGAGTCGCTAGATCAGAGGAGTTCATACCCAGATCTGTTCGTGCAATGGTAAGCGGCATTTGAAGGGCCTCTTCTTCACT

Reverse complement sequence

AGTGAAGAAGAGGCCCTTCAAATGCCGCTTACCATTGCACGAACAGATCTGGGTATGAACTCCTCTGATCTAGCGACTCTTATGCCCTAGATTCAAAATC[G/A]
TTCCCTAACCATTGCCGACATCTCCAACGAGCCTTTCATCCGCTCCTCTCCTTTCTCATTAGAAGAACATTGGATCTGGTCATTAGGCCAGATCCTACCC

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	73.70%	20.90%	0.11%	5.25%	NA
All Indica	2759	59.80%	34.50%	0.11%	5.51%	NA
All Japonica	1512	93.30%	0.90%	0.13%	5.69%	NA
Aus	269	98.10%	0.00%	0.00%	1.86%	NA
Indica I	595	83.50%	16.50%	0.00%	0.00%	NA
Indica II	465	31.60%	66.50%	0.22%	1.72%	NA
Indica III	913	60.90%	25.80%	0.00%	13.25%	NA
Indica Intermediate	786	57.40%	39.40%	0.25%	2.93%	NA
Temperate Japonica	767	90.70%	1.30%	0.26%	7.69%	NA
Tropical Japonica	504	94.60%	0.40%	0.00%	4.96%	NA
Japonica Intermediate	241	98.30%	0.80%	0.00%	0.83%	NA
VI/Aromatic	96	99.00%	0.00%	0.00%	1.04%	NA
Intermediate	90	71.10%	24.40%	0.00%	4.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0622854546	C -> T	LOC_Os06g38580.1	downstream_gene_variant ; 1869.0bp to feature; MODIFIER	silent_mutation	Average:50.282; most accessible tissue: Callus, score: 69.335	N	N	N	N
vg0622854546	C -> T	LOC_Os06g38564-LOC_Os06g38580	intergenic_region ; MODIFIER	silent_mutation	Average:50.282; most accessible tissue: Callus, score: 69.335	N	N	N	N
vg0622854546	C -> DEL	N	N	silent_mutation	Average:50.282; most accessible tissue: Callus, score: 69.335	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0622854546	NA	9.74E-06	mr1558	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