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Detailed information for vg0613864554:

Variant ID: vg0613864554 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 13864554
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AGGATATATGTGAGACTGAGGTAAAAGAGATGGAGACAGAGATTTTTATACAGGTTCGGGCCCCTGAGTTGTCAGGTAATAGCCCTACATCCTATTGGCC[A/G]
GAGCCGATGTTGCTTTTTATTCATCATAATCACACCAGTACAATATGTGGGTAGCCTATCTAACTGTTGTCGACATGTTGGTCTGAAGGTCTGACTCGTA

Reverse complement sequence

TACGAGTCAGACCTTCAGACCAACATGTCGACAACAGTTAGATAGGCTACCCACATATTGTACTGGTGTGATTATGATGAATAAAAAGCAACATCGGCTC[T/C]
GGCCAATAGGATGTAGGGCTATTACCTGACAACTCAGGGGCCCGAACCTGTATAAAAATCTCTGTCTCCATCTCTTTTACCTCAGTCTCACATATATCCT

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	35.50%	5.90%	1.33%	57.28%	NA
All Indica	2759	8.80%	1.70%	1.74%	87.71%	NA
All Japonica	1512	91.50%	6.20%	0.07%	2.31%	NA
Aus	269	1.90%	45.70%	1.12%	51.30%	NA
Indica I	595	16.60%	3.90%	1.68%	77.82%	NA
Indica II	465	9.20%	1.90%	3.66%	85.16%	NA
Indica III	913	2.20%	0.10%	1.10%	96.60%	NA
Indica Intermediate	786	10.40%	1.80%	1.40%	86.39%	NA
Temperate Japonica	767	97.00%	0.10%	0.13%	2.74%	NA
Tropical Japonica	504	82.90%	15.70%	0.00%	1.39%	NA
Japonica Intermediate	241	91.70%	5.40%	0.00%	2.90%	NA
VI/Aromatic	96	6.20%	4.20%	7.29%	82.29%	NA
Intermediate	90	45.60%	11.10%	4.44%	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
vg0613864554	A -> G	LOC_Os06g23710.1	upstream_gene_variant ; 3915.0bp to feature; MODIFIER	silent_mutation	Average:11.438; most accessible tissue: Callus, score: 40.199	N	N	N	N
vg0613864554	A -> G	LOC_Os06g23730.1	downstream_gene_variant ; 1300.0bp to feature; MODIFIER	silent_mutation	Average:11.438; most accessible tissue: Callus, score: 40.199	N	N	N	N
vg0613864554	A -> G	LOC_Os06g23720.1	intron_variant ; MODIFIER	silent_mutation	Average:11.438; most accessible tissue: Callus, score: 40.199	N	N	N	N
vg0613864554	A -> DEL	N	N	silent_mutation	Average:11.438; most accessible tissue: Callus, score: 40.199	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0613864554	5.48E-06	3.65E-07	mr1263	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
vg0613864554	5.48E-06	3.65E-07	mr1451	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