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Detailed information for vg0817059251:

Variant ID: vg0817059251 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 17059251
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ACAACGAAAAAACACGTGTTTTTGTTGTGCTATGATAAATTAACTAACTACTATTTTAAGACAAAAAAATATTTTACGTACAGATTTCATACGGTCTGTC[C/T]
GGATCGTGTCGACAATTAAAAAACACGTGGTTTTTTGTTGTCCTAAAAAATTAAATCACTGTTATTTAATTATATATATTTTTCATGTGGTCTGTCCGGA

Reverse complement sequence

TCCGGACAGACCACATGAAAAATATATATAATTAAATAACAGTGATTTAATTTTTTAGGACAACAAAAAACCACGTGTTTTTTAATTGTCGACACGATCC[G/A]
GACAGACCGTATGAAATCTGTACGTAAAATATTTTTTTGTCTTAAAATAGTAGTTAGTTAATTTATCATAGCACAACAAAAACACGTGTTTTTTCGTTGT

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	97.60%	0.10%	0.95%	1.35%	NA
All Indica	2759	98.80%	0.10%	0.80%	0.25%	NA
All Japonica	1512	94.60%	0.20%	1.46%	3.70%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	99.80%	0.20%	0.00%	0.00%	NA
Indica II	465	96.60%	0.20%	2.15%	1.08%	NA
Indica III	913	99.80%	0.00%	0.22%	0.00%	NA
Indica Intermediate	786	98.30%	0.10%	1.27%	0.25%	NA
Temperate Japonica	767	97.10%	0.10%	0.91%	1.83%	NA
Tropical Japonica	504	91.50%	0.40%	2.38%	5.75%	NA
Japonica Intermediate	241	93.40%	0.00%	1.24%	5.39%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	97.80%	0.00%	1.11%	1.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0817059251	C -> T	LOC_Os08g28010.1	upstream_gene_variant ; 1919.0bp to feature; MODIFIER	silent_mutation	Average:33.167; most accessible tissue: Zhenshan97 panicle, score: 57.341	N	N	N	N
vg0817059251	C -> T	LOC_Os08g27990.1	downstream_gene_variant ; 1462.0bp to feature; MODIFIER	silent_mutation	Average:33.167; most accessible tissue: Zhenshan97 panicle, score: 57.341	N	N	N	N
vg0817059251	C -> T	LOC_Os08g28000.1	downstream_gene_variant ; 970.0bp to feature; MODIFIER	silent_mutation	Average:33.167; most accessible tissue: Zhenshan97 panicle, score: 57.341	N	N	N	N
vg0817059251	C -> T	LOC_Os08g27990-LOC_Os08g28000	intergenic_region ; MODIFIER	silent_mutation	Average:33.167; most accessible tissue: Zhenshan97 panicle, score: 57.341	N	N	N	N
vg0817059251	C -> DEL	N	N	silent_mutation	Average:33.167; most accessible tissue: Zhenshan97 panicle, score: 57.341	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0817059251	2.26E-06	2.26E-06	mr1750	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