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Detailed information for vg1018095995:

Variant ID: vg1018095995 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 18095995
Reference Allele: A	Alternative Allele: G
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GTACTGGCTTTTCCATAGCGGCTGGCTTTGGTCCCGCTGGCTGGCTACGGTACCCGGCCTGGCTCAACTGTGGACGGGGATTGCTGGCTCTAGAGTTTTC[A/G]
GCTCTCACACTCATGCGAAAGTAATCGTCCATGTAGAAGGAAAAGAGATTGGAAGGAGGCCATCGAAAGGAAAGAGCAAACATAATGTGTAGCGTGGGGA

Reverse complement sequence

TCCCCACGCTACACATTATGTTTGCTCTTTCCTTTCGATGGCCTCCTTCCAATCTCTTTTCCTTCTACATGGACGATTACTTTCGCATGAGTGTGAGAGC[T/C]
GAAAACTCTAGAGCCAGCAATCCCCGTCCACAGTTGAGCCAGGCCGGGTACCGTAGCCAGCCAGCGGGACCAAAGCCAGCCGCTATGGAAAAGCCAGTAC

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	70.00%	29.90%	0.02%	0.00%	NA
All Indica	2759	98.80%	1.20%	0.00%	0.00%	NA
All Japonica	1512	16.90%	83.10%	0.07%	0.00%	NA
Aus	269	99.60%	0.40%	0.00%	0.00%	NA
Indica I	595	98.20%	1.80%	0.00%	0.00%	NA
Indica II	465	98.70%	1.30%	0.00%	0.00%	NA
Indica III	913	99.70%	0.30%	0.00%	0.00%	NA
Indica Intermediate	786	98.20%	1.80%	0.00%	0.00%	NA
Temperate Japonica	767	2.10%	97.90%	0.00%	0.00%	NA
Tropical Japonica	504	42.50%	57.30%	0.20%	0.00%	NA
Japonica Intermediate	241	10.40%	89.60%	0.00%	0.00%	NA
VI/Aromatic	96	9.40%	90.60%	0.00%	0.00%	NA
Intermediate	90	58.90%	41.10%	0.00%	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
vg1018095995	A -> G	LOC_Os10g33960.1	downstream_gene_variant ; 3495.0bp to feature; MODIFIER	silent_mutation	Average:55.605; most accessible tissue: Zhenshan97 panicle, score: 73.605	N	N	N	N
vg1018095995	A -> G	LOC_Os10g33960.4	downstream_gene_variant ; 3496.0bp to feature; MODIFIER	silent_mutation	Average:55.605; most accessible tissue: Zhenshan97 panicle, score: 73.605	N	N	N	N
vg1018095995	A -> G	LOC_Os10g33960.2	downstream_gene_variant ; 3496.0bp to feature; MODIFIER	silent_mutation	Average:55.605; most accessible tissue: Zhenshan97 panicle, score: 73.605	N	N	N	N
vg1018095995	A -> G	LOC_Os10g33960-LOC_Os10g33970	intergenic_region ; MODIFIER	silent_mutation	Average:55.605; most accessible tissue: Zhenshan97 panicle, score: 73.605	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1018095995	NA	2.18E-56	mr1019	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
vg1018095995	8.46E-06	NA	mr1490	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
vg1018095995	NA	9.08E-09	mr1514	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
vg1018095995	NA	7.70E-07	mr1781	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
vg1018095995	NA	8.46E-40	mr1873	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
vg1018095995	NA	1.64E-12	mr1940	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
vg1018095995	NA	6.10E-22	mr1276_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
vg1018095995	NA	8.77E-19	mr1336_2	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