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Detailed information for vg0716086173:

Variant ID: vg0716086173 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 16086173
Reference Allele: A	Alternative Allele: T
Primary Allele: A	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TTGGGCAAAATTACGTTGCCTGTGACTTTCGGCCAAGCAAATAACTTCCGAACGGAGCAAATCACCTTCCGGGGTTTCTGATTCCGATTCCGAAAAAAAT[A/T]
TGAAAATGAAAACGATAAAGATGATTTCCATCCGTTTCCATACCGTTTTCACCTATAGTGCTCAAGATGCCAGGACCGAAGGGAACAATCACTATTCAAG

Reverse complement sequence

CTTGAATAGTGATTGTTCCCTTCGGTCCTGGCATCTTGAGCACTATAGGTGAAAACGGTATGGAAACGGATGGAAATCATCTTTATCGTTTTCATTTTCA[T/A]
ATTTTTTTCGGAATCGGAATCAGAAACCCCGGAAGGTGATTTGCTCCGTTCGGAAGTTATTTGCTTGGCCGAAAGTCACAGGCAACGTAATTTTGCCCAA

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	62.20%	1.90%	2.50%	33.41%	NA
All Indica	2759	45.30%	0.20%	2.50%	52.05%	NA
All Japonica	1512	92.00%	5.50%	1.98%	0.53%	NA
Aus	269	52.40%	0.00%	5.95%	41.64%	NA
Indica I	595	59.70%	0.00%	1.34%	38.99%	NA
Indica II	465	23.40%	0.90%	3.01%	72.69%	NA
Indica III	913	37.00%	0.00%	3.83%	59.15%	NA
Indica Intermediate	786	56.90%	0.10%	1.53%	41.48%	NA
Temperate Japonica	767	88.10%	8.50%	2.87%	0.52%	NA
Tropical Japonica	504	97.40%	1.00%	1.39%	0.20%	NA
Japonica Intermediate	241	92.90%	5.40%	0.41%	1.24%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	70.00%	1.10%	3.33%	25.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0716086173	A -> DEL	N	N	silent_mutation	Average:6.433; most accessible tissue: Callus, score: 11.699	N	N	N	N
vg0716086173	A -> T	LOC_Os07g27530.1	downstream_gene_variant ; 4141.0bp to feature; MODIFIER	silent_mutation	Average:6.433; most accessible tissue: Callus, score: 11.699	N	N	N	N
vg0716086173	A -> T	LOC_Os07g27520.1	intron_variant ; MODIFIER	silent_mutation	Average:6.433; most accessible tissue: Callus, score: 11.699	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0716086173	2.08E-06	6.73E-08	mr1844	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