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Detailed information for vg0805055259:

Variant ID: vg0805055259 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 5055259
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ATACTCCCTCCGTTTCAAAATATTTGACGCCGTTGACTTTTTTAAATATGTTTGACCGTTCGTCTTATTTAAAAAATTTAAGTAATTATTACATCTTTTC[C/T]
TATCATTTGATTCATTGTTAAATATATTTTTATGTAGGCATATCATTTTACATATTTTATAAAAGTTTTTGAATAAGACGAACGGTTAAACATGTGCTAA

Reverse complement sequence

TTAGCACATGTTTAACCGTTCGTCTTATTCAAAAACTTTTATAAAATATGTAAAATGATATGCCTACATAAAAATATATTTAACAATGAATCAAATGATA[G/A]
GAAAAGATGTAATAATTACTTAAATTTTTTAAATAAGACGAACGGTCAAACATATTTAAAAAAGTCAACGGCGTCAAATATTTTGAAACGGAGGGAGTAT

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	63.70%	3.30%	0.63%	32.37%	NA
All Indica	2759	58.10%	0.10%	0.83%	40.96%	NA
All Japonica	1512	79.50%	10.00%	0.20%	10.32%	NA
Aus	269	43.10%	0.00%	0.37%	56.51%	NA
Indica I	595	92.80%	0.00%	0.17%	7.06%	NA
Indica II	465	36.10%	0.00%	1.51%	62.37%	NA
Indica III	913	45.20%	0.20%	0.66%	53.89%	NA
Indica Intermediate	786	59.70%	0.30%	1.15%	38.93%	NA
Temperate Japonica	767	90.90%	1.40%	0.26%	7.43%	NA
Tropical Japonica	504	69.40%	19.40%	0.00%	11.11%	NA
Japonica Intermediate	241	64.30%	17.40%	0.41%	17.84%	NA
VI/Aromatic	96	33.30%	0.00%	2.08%	64.58%	NA
Intermediate	90	63.30%	2.20%	1.11%	33.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0805055259	C -> T	LOC_Os08g08720.1	downstream_gene_variant ; 1022.0bp to feature; MODIFIER	silent_mutation	Average:26.731; most accessible tissue: Zhenshan97 root, score: 83.087	N	N	N	N
vg0805055259	C -> T	LOC_Os08g08730.1	downstream_gene_variant ; 3693.0bp to feature; MODIFIER	silent_mutation	Average:26.731; most accessible tissue: Zhenshan97 root, score: 83.087	N	N	N	N
vg0805055259	C -> T	LOC_Os08g08720-LOC_Os08g08730	intergenic_region ; MODIFIER	silent_mutation	Average:26.731; most accessible tissue: Zhenshan97 root, score: 83.087	N	N	N	N
vg0805055259	C -> DEL	N	N	silent_mutation	Average:26.731; most accessible tissue: Zhenshan97 root, score: 83.087	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0805055259	1.64E-06	NA	mr1125	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
vg0805055259	NA	5.96E-06	mr1738_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