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Detailed information for vg0206377668:

Variant ID: vg0206377668 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 6377668
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GAGCGCCTCGCGCCCCCCGGCAAAACCTTCGCGTTGCTGTCGAAGAAGAACAGAGAAAGAGAGATTGACAAGTGGGCCCATGGACAAACTTGTCTTTAAC[T/C]
TAAGTTTCTCTCTCCGTTTTCATCGAAAATAATAAAATAATGGGAGGAGTGTCCAGTAGCTAATTACCACTTTTTTACCGTGTCCACGAGCAAATACACG

Reverse complement sequence

CGTGTATTTGCTCGTGGACACGGTAAAAAAGTGGTAATTAGCTACTGGACACTCCTCCCATTATTTTATTATTTTCGATGAAAACGGAGAGAGAAACTTA[A/G]
GTTAAAGACAAGTTTGTCCATGGGCCCACTTGTCAATCTCTCTTTCTCTGTTCTTCTTCGACAGCAACGCGAAGGTTTTGCCGGGGGGCGCGAGGCGCTC

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	58.70%	35.10%	3.07%	3.15%	NA
All Indica	2759	87.80%	3.80%	3.52%	4.89%	NA
All Japonica	1512	2.00%	96.30%	1.32%	0.40%	NA
Aus	269	81.00%	11.90%	6.69%	0.37%	NA
Indica I	595	83.50%	4.50%	5.71%	6.22%	NA
Indica II	465	75.50%	5.80%	5.59%	13.12%	NA
Indica III	913	95.70%	1.90%	1.64%	0.77%	NA
Indica Intermediate	786	89.20%	4.20%	2.80%	3.82%	NA
Temperate Japonica	767	1.40%	97.30%	0.52%	0.78%	NA
Tropical Japonica	504	2.00%	95.60%	2.38%	0.00%	NA
Japonica Intermediate	241	3.70%	94.60%	1.66%	0.00%	NA
VI/Aromatic	96	68.80%	27.10%	2.08%	2.08%	NA
Intermediate	90	41.10%	44.40%	8.89%	5.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0206377668	T -> DEL	N	N	silent_mutation	Average:39.38; most accessible tissue: Zhenshan97 flower, score: 59.755	N	N	N	N
vg0206377668	T -> C	LOC_Os02g12250.1	upstream_gene_variant ; 4408.0bp to feature; MODIFIER	silent_mutation	Average:39.38; most accessible tissue: Zhenshan97 flower, score: 59.755	N	N	N	N
vg0206377668	T -> C	LOC_Os02g12230.1	downstream_gene_variant ; 1738.0bp to feature; MODIFIER	silent_mutation	Average:39.38; most accessible tissue: Zhenshan97 flower, score: 59.755	N	N	N	N
vg0206377668	T -> C	LOC_Os02g12240.1	downstream_gene_variant ; 639.0bp to feature; MODIFIER	silent_mutation	Average:39.38; most accessible tissue: Zhenshan97 flower, score: 59.755	N	N	N	N
vg0206377668	T -> C	LOC_Os02g12240-LOC_Os02g12250	intergenic_region ; MODIFIER	silent_mutation	Average:39.38; most accessible tissue: Zhenshan97 flower, score: 59.755	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0206377668	NA	5.79E-44	mr1136	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
vg0206377668	NA	2.03E-10	mr1175	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
vg0206377668	NA	9.92E-27	mr1309	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
vg0206377668	NA	3.37E-14	mr1361	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
vg0206377668	NA	1.12E-35	mr1448	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
vg0206377668	NA	8.09E-28	mr1638	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