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Detailed information for vg0905593689:

Variant ID: vg0905593689 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 5593689
Reference Allele: A	Alternative Allele: T
Primary Allele: A	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CCCCCTCCCCAATGCCCCTGCGTGATTAGCGGATCGGATCCCGCTAATTACCCATATTAACGTTAATTACCTTGATTAGTATTTTTTTAGTACGCAAAAA[A/T]
TTGGGATAAGTATGGAGAATTAACAACAATAAACTTTCAACGAAGGTTTGAAAACTTTTACGTGAAGATTTGGAACATTCAAATCAAGATTTTTTGAAAT

Reverse complement sequence

ATTTCAAAAAATCTTGATTTGAATGTTCCAAATCTTCACGTAAAAGTTTTCAAACCTTCGTTGAAAGTTTATTGTTGTTAATTCTCCATACTTATCCCAA[T/A]
TTTTTGCGTACTAAAAAAATACTAATCAAGGTAATTAACGTTAATATGGGTAATTAGCGGGATCCGATCCGCTAATCACGCAGGGGCATTGGGGAGGGGG

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	94.70%	0.20%	3.62%	1.44%	NA
All Indica	2759	97.20%	0.10%	1.92%	0.76%	NA
All Japonica	1512	99.20%	0.00%	0.73%	0.07%	NA
Aus	269	61.30%	2.20%	19.33%	17.10%	NA
Indica I	595	98.70%	0.20%	1.18%	0.00%	NA
Indica II	465	99.60%	0.20%	0.22%	0.00%	NA
Indica III	913	97.40%	0.00%	1.86%	0.77%	NA
Indica Intermediate	786	94.70%	0.00%	3.56%	1.78%	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	95.00%	0.00%	4.56%	0.41%	NA
VI/Aromatic	96	49.00%	1.00%	50.00%	0.00%	NA
Intermediate	90	91.10%	1.10%	7.78%	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
vg0905593689	A -> DEL	N	N	silent_mutation	Average:37.443; most accessible tissue: Minghui63 root, score: 65.279	N	N	N	N
vg0905593689	A -> T	LOC_Os09g10274.1	upstream_gene_variant ; 4955.0bp to feature; MODIFIER	silent_mutation	Average:37.443; most accessible tissue: Minghui63 root, score: 65.279	N	N	N	N
vg0905593689	A -> T	LOC_Os09g10270.1	downstream_gene_variant ; 1097.0bp to feature; MODIFIER	silent_mutation	Average:37.443; most accessible tissue: Minghui63 root, score: 65.279	N	N	N	N
vg0905593689	A -> T	LOC_Os09g10260-LOC_Os09g10270	intergenic_region ; MODIFIER	silent_mutation	Average:37.443; most accessible tissue: Minghui63 root, score: 65.279	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0905593689	7.84E-06	NA	mr1200_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