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Detailed information for vg0721709577:

Variant ID: vg0721709577 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 21709577
Reference Allele: T	Alternative Allele: A
Primary Allele: T	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GATCTAAATATATTTTCATGCTTTTATGTCCCTAGCACAACCTTACTTGTTCCTAGCTAACTAAATATGTGATTAACACAATTTAATTAGCTATTATATA[T/A]
AAATATCATCACACAGTTACATTAACCACCATAAATAGATCGATAGACCAGTGTTTTTGGTAATACAACTTGTGTTATACTCTAATTATTTATTTCGTGA

Reverse complement sequence

TCACGAAATAAATAATTAGAGTATAACACAAGTTGTATTACCAAAAACACTGGTCTATCGATCTATTTATGGTGGTTAATGTAACTGTGTGATGATATTT[A/T]
TATATAATAGCTAATTAAATTGTGTTAATCACATATTTAGTTAGCTAGGAACAAGTAAGGTTGTGCTAGGGACATAAAAGCATGAAAATATATTTAGATC

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	93.30%	6.70%	0.02%	0.00%	NA
All Indica	2759	93.30%	6.70%	0.04%	0.00%	NA
All Japonica	1512	100.00%	0.00%	0.00%	0.00%	NA
Aus	269	52.00%	48.00%	0.00%	0.00%	NA
Indica I	595	96.60%	3.40%	0.00%	0.00%	NA
Indica II	465	98.90%	1.10%	0.00%	0.00%	NA
Indica III	913	89.60%	10.40%	0.00%	0.00%	NA
Indica Intermediate	786	91.60%	8.30%	0.13%	0.00%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	95.60%	4.40%	0.00%	0.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0721709577	T -> A	LOC_Os07g36290.1	downstream_gene_variant ; 3910.0bp to feature; MODIFIER	silent_mutation	Average:29.179; most accessible tissue: Callus, score: 58.012	N	N	N	N
vg0721709577	T -> A	LOC_Os07g36300.1	intron_variant ; MODIFIER	silent_mutation	Average:29.179; most accessible tissue: Callus, score: 58.012	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0721709577	4.76E-06	NA	mr1098_2	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
vg0721709577	6.36E-06	NA	mr1123_2	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