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Detailed information for vg0725076744:

Variant ID: vg0725076744 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 25076744
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CCTCTTTCAACTCCCCTTAGGAGTTGCACTCGGTTTCGCAAGCTCTTGCATGCCATACTATACCCCCTACCCCCAGTAACCACCTTAGCGTGTTACTGAT[A/G]
TATGCTACTTTTCTTCTAATATATTGACGTGCAAATATTTTGCGCGTTTGGAAAAAAACACAACATCAAACATAAATTTTGCTTGGTTGACCAAAATTCA

Reverse complement sequence

TGAATTTTGGTCAACCAAGCAAAATTTATGTTTGATGTTGTGTTTTTTTCCAAACGCGCAAAATATTTGCACGTCAATATATTAGAAGAAAAGTAGCATA[T/C]
ATCAGTAACACGCTAAGGTGGTTACTGGGGGTAGGGGGTATAGTATGGCATGCAAGAGCTTGCGAAACCGAGTGCAACTCCTAAGGGGAGTTGAAAGAGG

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	20.90%	9.50%	0.66%	68.96%	NA
All Indica	2759	2.50%	6.50%	0.72%	90.32%	NA
All Japonica	1512	53.80%	0.10%	0.53%	45.50%	NA
Aus	269	1.10%	92.90%	0.00%	5.95%	NA
Indica I	595	2.90%	16.60%	0.17%	80.34%	NA
Indica II	465	2.80%	0.40%	0.65%	96.13%	NA
Indica III	913	1.20%	2.10%	0.33%	96.39%	NA
Indica Intermediate	786	3.60%	7.40%	1.65%	87.40%	NA
Temperate Japonica	767	42.80%	0.10%	0.26%	56.84%	NA
Tropical Japonica	504	58.30%	0.00%	1.19%	40.48%	NA
Japonica Intermediate	241	79.70%	0.40%	0.00%	19.92%	NA
VI/Aromatic	96	78.10%	5.20%	0.00%	16.67%	NA
Intermediate	90	30.00%	14.40%	3.33%	52.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0725076744	A -> DEL	N	N	silent_mutation	Average:10.491; most accessible tissue: Callus, score: 70.734	N	N	N	N
vg0725076744	A -> G	LOC_Os07g41860.1	upstream_gene_variant ; 373.0bp to feature; MODIFIER	silent_mutation	Average:10.491; most accessible tissue: Callus, score: 70.734	N	N	N	N
vg0725076744	A -> G	LOC_Os07g41850-LOC_Os07g41860	intergenic_region ; MODIFIER	silent_mutation	Average:10.491; most accessible tissue: Callus, score: 70.734	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0725076744	1.76E-06	1.76E-06	mr1644	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