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Detailed information for vg0607084144:

Variant ID: vg0607084144 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 7084144
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TGGGTCCGCGATAAATCAGCCACCACGTTGGACAAAACCGCCTGAGGACCCAAAATGATGGCATACATCTGATTTTGCGGTGGGGATGATTTTGTAATCT[G/A]
ATGATAAGATGAGGGACCTTGTATGTACTTTTTTTCCCTTTAAGCTCTACGTACTGCTGCCTAGTTCGGCCTATTTCCGTGGAGGGCTAGAGGCCCAACT

Reverse complement sequence

AGTTGGGCCTCTAGCCCTCCACGGAAATAGGCCGAACTAGGCAGCAGTACGTAGAGCTTAAAGGGAAAAAAAGTACATACAAGGTCCCTCATCTTATCAT[C/T]
AGATTACAAAATCATCCCCACCGCAAAATCAGATGTATGCCATCATTTTGGGTCCTCAGGCGGTTTTGTCCAACGTGGTGGCTGATTTATCGCGGACCCA

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	44.80%	4.30%	1.02%	49.94%	NA
All Indica	2759	27.50%	0.00%	1.49%	70.97%	NA
All Japonica	1512	85.80%	12.60%	0.26%	1.26%	NA
Aus	269	0.70%	0.00%	0.00%	99.26%	NA
Indica I	595	9.40%	0.00%	2.52%	88.07%	NA
Indica II	465	64.50%	0.00%	1.29%	34.19%	NA
Indica III	913	18.10%	0.00%	0.22%	81.71%	NA
Indica Intermediate	786	30.30%	0.10%	2.29%	67.30%	NA
Temperate Japonica	767	99.00%	0.00%	0.00%	1.04%	NA
Tropical Japonica	504	61.50%	36.70%	0.79%	0.99%	NA
Japonica Intermediate	241	95.00%	2.50%	0.00%	2.49%	NA
VI/Aromatic	96	10.40%	0.00%	1.04%	88.54%	NA
Intermediate	90	53.30%	10.00%	2.22%	34.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0607084144	G -> A	LOC_Os06g12940.1	upstream_gene_variant ; 1709.0bp to feature; MODIFIER	silent_mutation	Average:15.733; most accessible tissue: Callus, score: 94.162	N	N	N	N
vg0607084144	G -> A	LOC_Os06g12950.1	upstream_gene_variant ; 946.0bp to feature; MODIFIER	silent_mutation	Average:15.733; most accessible tissue: Callus, score: 94.162	N	N	N	N
vg0607084144	G -> A	LOC_Os06g12940-LOC_Os06g12950	intergenic_region ; MODIFIER	silent_mutation	Average:15.733; most accessible tissue: Callus, score: 94.162	N	N	N	N
vg0607084144	G -> DEL	N	N	silent_mutation	Average:15.733; most accessible tissue: Callus, score: 94.162	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0607084144	2.01E-06	2.01E-06	mr1335_2	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
vg0607084144	NA	2.18E-07	mr1363_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