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Detailed information for vg0102718620:

Variant ID: vg0102718620 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 2718620
Reference Allele: A	Alternative Allele: C
Primary Allele: A	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TTTTTTATAATTAGTATTTTTATTGTTGTTCGATAATAAAACATGATTAATACTTATGCGTGACTTATTTTTTAAATTTTTTTCATAATTTTTTTAAATA[A/C]
GACGGACGGTCAAACGTTGGACACGAAAATCCAGGGTTTGTCTTTTTTTTTTTAATGGAGGGAGTAGGTTTTAGCTCGAGCTTGTATAATTTGGGCAGCT

Reverse complement sequence

AGCTGCCCAAATTATACAAGCTCGAGCTAAAACCTACTCCCTCCATTAAAAAAAAAAAGACAAACCCTGGATTTTCGTGTCCAACGTTTGACCGTCCGTC[T/G]
TATTTAAAAAAATTATGAAAAAAATTTAAAAAATAAGTCACGCATAAGTATTAATCATGTTTTATTATCGAACAACAATAAAAATACTAATTATAAAAAA

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	88.40%	6.90%	1.12%	3.55%	NA
All Indica	2759	98.40%	0.70%	0.18%	0.72%	NA
All Japonica	1512	78.80%	20.20%	0.99%	0.07%	NA
Aus	269	37.50%	0.00%	11.90%	50.56%	NA
Indica I	595	98.50%	1.50%	0.00%	0.00%	NA
Indica II	465	96.80%	0.60%	1.08%	1.51%	NA
Indica III	913	99.60%	0.00%	0.00%	0.44%	NA
Indica Intermediate	786	98.00%	0.90%	0.00%	1.15%	NA
Temperate Japonica	767	64.50%	33.60%	1.83%	0.00%	NA
Tropical Japonica	504	98.80%	1.00%	0.00%	0.20%	NA
Japonica Intermediate	241	82.20%	17.40%	0.41%	0.00%	NA
VI/Aromatic	96	90.60%	0.00%	0.00%	9.38%	NA
Intermediate	90	94.40%	2.20%	1.11%	2.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0102718620	A -> DEL	N	N	silent_mutation	Average:67.67; most accessible tissue: Zhenshan97 flag leaf, score: 85.259	N	N	N	N
vg0102718620	A -> C	LOC_Os01g05694.1	upstream_gene_variant ; 592.0bp to feature; MODIFIER	silent_mutation	Average:67.67; most accessible tissue: Zhenshan97 flag leaf, score: 85.259	N	N	N	N
vg0102718620	A -> C	LOC_Os01g05710.1	upstream_gene_variant ; 3898.0bp to feature; MODIFIER	silent_mutation	Average:67.67; most accessible tissue: Zhenshan97 flag leaf, score: 85.259	N	N	N	N
vg0102718620	A -> C	LOC_Os01g05680.1	downstream_gene_variant ; 2545.0bp to feature; MODIFIER	silent_mutation	Average:67.67; most accessible tissue: Zhenshan97 flag leaf, score: 85.259	N	N	N	N
vg0102718620	A -> C	LOC_Os01g05680-LOC_Os01g05694	intergenic_region ; MODIFIER	silent_mutation	Average:67.67; most accessible tissue: Zhenshan97 flag leaf, score: 85.259	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0102718620	NA	5.39E-06	mr1092	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
vg0102718620	8.99E-07	8.99E-07	mr1914	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
vg0102718620	NA	8.40E-07	mr1354_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
vg0102718620	NA	1.80E-06	mr1902_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