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Detailed information for vg0109760110:

Variant ID: vg0109760110 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 9760110
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AAAAAGTGATAAATAAATTAAGAATAGGGTTTACGAGGTACTAAGGCACGAACGCCTAAATATTTAATAACCTCGAGGCAGTTCAGATTCATGATATTTT[C/T]
AACCATATCATTTTTGGCATCAATCTGAACAACGCCTAAATATAGAGTGAGAATTAATATATATACAATCCAAAGGACAAAAATAAAGACATAAACAGGG

Reverse complement sequence

CCCTGTTTATGTCTTTATTTTTGTCCTTTGGATTGTATATATATTAATTCTCACTCTATATTTAGGCGTTGTTCAGATTGATGCCAAAAATGATATGGTT[G/A]
AAAATATCATGAATCTGAACTGCCTCGAGGTTATTAAATATTTAGGCGTTCGTGCCTTAGTACCTCGTAAACCCTATTCTTAATTTATTTATCACTTTTT

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	92.70%	5.80%	1.59%	0.00%	NA
All Indica	2759	87.80%	9.60%	2.57%	0.00%	NA
All Japonica	1512	99.80%	0.10%	0.13%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	95.30%	0.00%	4.71%	0.00%	NA
Indica II	465	84.30%	13.30%	2.37%	0.00%	NA
Indica III	913	84.70%	14.60%	0.77%	0.00%	NA
Indica Intermediate	786	87.90%	8.90%	3.18%	0.00%	NA
Temperate Japonica	767	99.90%	0.00%	0.13%	0.00%	NA
Tropical Japonica	504	99.60%	0.20%	0.20%	0.00%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	99.00%	1.00%	0.00%	0.00%	NA
Intermediate	90	92.20%	5.60%	2.22%	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
vg0109760110	C -> T	LOC_Os01g17040.1	upstream_gene_variant ; 4863.0bp to feature; MODIFIER	silent_mutation	Average:40.557; most accessible tissue: Zhenshan97 panicle, score: 59.59	N	N	N	N
vg0109760110	C -> T	LOC_Os01g17030.1	downstream_gene_variant ; 4313.0bp to feature; MODIFIER	silent_mutation	Average:40.557; most accessible tissue: Zhenshan97 panicle, score: 59.59	N	N	N	N
vg0109760110	C -> T	LOC_Os01g17030-LOC_Os01g17040	intergenic_region ; MODIFIER	silent_mutation	Average:40.557; most accessible tissue: Zhenshan97 panicle, score: 59.59	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0109760110	6.99E-06	6.99E-06	mr1753	Ind_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