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Detailed information for vg0408360478:

Variant ID: vg0408360478 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 8360478
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, T: 0.01, others allele: 0.00, population size: 108. )

Flanking Sequence (100 bp) in Reference Genome:

CGACGACGCTAGGTAAGATTGAACGGAATAGATTACATAGATGAATTGATGATTGCAGAAGCAAACCCATCAACAGAGAGTGAGAACGGAGTACCAGCGG[C/T]
GCAACGGCGACGACGGCGATGGCGGGAGGCGGCGGCACTTGCCGGCGGCTGTGGGACAGCAAGCGGCGGCGGCGGCGGCTGCGGCTAGAGCTAGAGCAAA

Reverse complement sequence

TTTGCTCTAGCTCTAGCCGCAGCCGCCGCCGCCGCCGCTTGCTGTCCCACAGCCGCCGGCAAGTGCCGCCGCCTCCCGCCATCGCCGTCGTCGCCGTTGC[G/A]
CCGCTGGTACTCCGTTCTCACTCTCTGTTGATGGGTTTGCTTCTGCAATCATCAATTCATCTATGTAATCTATTCCGTTCAATCTTACCTAGCGTCGTCG

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	61.40%	26.50%	7.77%	4.34%	NA
All Indica	2759	42.00%	44.70%	8.88%	4.42%	NA
All Japonica	1512	88.80%	0.40%	6.55%	4.30%	NA
Aus	269	88.50%	0.00%	6.32%	5.20%	NA
Indica I	595	18.80%	65.90%	11.93%	3.36%	NA
Indica II	465	36.80%	40.40%	12.90%	9.89%	NA
Indica III	913	58.40%	35.90%	2.63%	3.07%	NA
Indica Intermediate	786	43.50%	41.50%	11.45%	3.56%	NA
Temperate Japonica	767	81.40%	0.30%	10.56%	7.82%	NA
Tropical Japonica	504	98.40%	0.40%	0.60%	0.60%	NA
Japonica Intermediate	241	92.10%	0.80%	6.22%	0.83%	NA
VI/Aromatic	96	99.00%	0.00%	1.04%	0.00%	NA
Intermediate	90	74.40%	15.60%	5.56%	4.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0408360478	C -> DEL	N	N	silent_mutation	Average:56.394; most accessible tissue: Zhenshan97 young leaf, score: 84.235	N	N	N	N
vg0408360478	C -> T	LOC_Os04g14860.1	upstream_gene_variant ; 1958.0bp to feature; MODIFIER	silent_mutation	Average:56.394; most accessible tissue: Zhenshan97 young leaf, score: 84.235	N	N	N	N
vg0408360478	C -> T	LOC_Os04g14870.1	upstream_gene_variant ; 3349.0bp to feature; MODIFIER	silent_mutation	Average:56.394; most accessible tissue: Zhenshan97 young leaf, score: 84.235	N	N	N	N
vg0408360478	C -> T	LOC_Os04g14860-LOC_Os04g14870	intergenic_region ; MODIFIER	silent_mutation	Average:56.394; most accessible tissue: Zhenshan97 young leaf, score: 84.235	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0408360478	NA	5.11E-06	mr1386	Ind_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
vg0408360478	NA	4.11E-09	mr1403	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
vg0408360478	NA	4.81E-07	mr1403	Ind_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
vg0408360478	NA	2.32E-06	mr1414	Ind_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
vg0408360478	NA	3.68E-06	mr1818	Ind_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
vg0408360478	6.51E-06	NA	mr1830	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
vg0408360478	4.47E-06	8.77E-11	mr1830	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
vg0408360478	1.29E-08	NA	mr1846	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
vg0408360478	1.20E-08	2.76E-16	mr1846	Ind_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
vg0408360478	NA	7.00E-07	mr1925	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
vg0408360478	NA	7.09E-08	mr1608_2	Ind_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
vg0408360478	2.94E-06	NA	mr1830_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
vg0408360478	8.61E-06	1.11E-14	mr1830_2	Ind_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
vg0408360478	6.51E-10	9.25E-14	mr1846_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
vg0408360478	4.40E-09	5.10E-29	mr1846_2	Ind_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