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Detailed information for vg0604453219:

Variant ID: vg0604453219 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 4453219
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CATACCCAATAGTGATCAACTAAGCTCGGTAGGGCCCACCACATACCATGCCTTATACGGAATCATACCTCGTATATAGAAGAAGTTCCGGATAAGGAAG[G/A]
ACAAATAGAGTTCTATATGGAAACGACAAGGACTACTCGGATTGTATCCATATTGGTCTCCCAAGTTCTACTTGGACAAGGGGGCATCTATGGGTAGAAA

Reverse complement sequence

TTTCTACCCATAGATGCCCCCTTGTCCAAGTAGAACTTGGGAGACCAATATGGATACAATCCGAGTAGTCCTTGTCGTTTCCATATAGAACTCTATTTGT[C/T]
CTTCCTTATCCGGAACTTCTTCTATATACGAGGTATGATTCCGTATAAGGCATGGTATGTGGTGGGCCCTACCGAGCTTAGTTGATCACTATTGGGTATG

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	46.10%	0.20%	0.38%	53.32%	NA
All Indica	2759	35.40%	0.40%	0.51%	63.75%	NA
All Japonica	1512	66.90%	0.00%	0.20%	32.94%	NA
Aus	269	45.70%	0.40%	0.00%	53.90%	NA
Indica I	595	22.70%	0.50%	0.34%	76.47%	NA
Indica II	465	37.40%	0.40%	0.00%	62.15%	NA
Indica III	913	43.40%	0.20%	0.77%	55.64%	NA
Indica Intermediate	786	34.50%	0.40%	0.64%	64.50%	NA
Temperate Japonica	767	95.00%	0.00%	0.00%	4.95%	NA
Tropical Japonica	504	31.00%	0.00%	0.60%	68.45%	NA
Japonica Intermediate	241	52.30%	0.00%	0.00%	47.72%	NA
VI/Aromatic	96	28.10%	0.00%	0.00%	71.88%	NA
Intermediate	90	44.40%	0.00%	1.11%	54.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0604453219	G -> A	LOC_Os06g08870.1	downstream_gene_variant ; 3446.0bp to feature; MODIFIER	silent_mutation	Average:13.344; most accessible tissue: Callus, score: 55.807	N	N	N	N
vg0604453219	G -> A	LOC_Os06g08870-LOC_Os06g08880	intergenic_region ; MODIFIER	silent_mutation	Average:13.344; most accessible tissue: Callus, score: 55.807	N	N	N	N
vg0604453219	G -> DEL	N	N	silent_mutation	Average:13.344; most accessible tissue: Callus, score: 55.807	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0604453219	3.64E-06	1.12E-06	mr1158_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