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Detailed information for vg0616479820:

Variant ID: vg0616479820 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 16479820
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, others allele: 0.00, population size: 254. )

Flanking Sequence (100 bp) in Reference Genome:

TCAAAGGAATTGTGTTTGGGATCTGTGTGACTTGCCTTGCAATAATCGGTCTTCACTTAATCTTCTGAATCACTTCCAACGCACTCACGAACCTTCGCAA[C/T]
GACGGAAACGACAAGCTAACACGCAAAACGAAGAAAAAGACTAATAAAAACCAAATAAACAGTACATAAAAAGCAAACAAACATGTAGATCATGATTTTA

Reverse complement sequence

TAAAATCATGATCTACATGTTTGTTTGCTTTTTATGTACTGTTTATTTGGTTTTTATTAGTCTTTTTCTTCGTTTTGCGTGTTAGCTTGTCGTTTCCGTC[G/A]
TTGCGAAGGTTCGTGAGTGCGTTGGAAGTGATTCAGAAGATTAAGTGAAGACCGATTATTGCAAGGCAAGTCACACAGATCCCAAACACAATTCCTTTGA

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	71.90%	28.10%	0.04%	0.00%	NA
All Indica	2759	54.50%	45.50%	0.04%	0.00%	NA
All Japonica	1512	98.60%	1.30%	0.07%	0.00%	NA
Aus	269	86.60%	13.40%	0.00%	0.00%	NA
Indica I	595	88.20%	11.80%	0.00%	0.00%	NA
Indica II	465	76.60%	23.40%	0.00%	0.00%	NA
Indica III	913	15.80%	84.10%	0.11%	0.00%	NA
Indica Intermediate	786	60.90%	39.10%	0.00%	0.00%	NA
Temperate Japonica	767	98.00%	1.80%	0.13%	0.00%	NA
Tropical Japonica	504	99.20%	0.80%	0.00%	0.00%	NA
Japonica Intermediate	241	99.20%	0.80%	0.00%	0.00%	NA
VI/Aromatic	96	99.00%	1.00%	0.00%	0.00%	NA
Intermediate	90	81.10%	18.90%	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
vg0616479820	C -> T	LOC_Os06g28880.2	5_prime_UTR_variant ; 839.0bp to feature; MODIFIER	silent_mutation	Average:44.092; most accessible tissue: Zhenshan97 flower, score: 56.224	N	N	N	N
vg0616479820	C -> T	LOC_Os06g28880.1	upstream_gene_variant ; 1559.0bp to feature; MODIFIER	silent_mutation	Average:44.092; most accessible tissue: Zhenshan97 flower, score: 56.224	N	N	N	N
vg0616479820	C -> T	LOC_Os06g28890.1	upstream_gene_variant ; 1374.0bp to feature; MODIFIER	silent_mutation	Average:44.092; most accessible tissue: Zhenshan97 flower, score: 56.224	N	N	N	N
vg0616479820	C -> T	LOC_Os06g28880.3	intron_variant ; MODIFIER	silent_mutation	Average:44.092; most accessible tissue: Zhenshan97 flower, score: 56.224	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0616479820	NA	2.14E-07	mr1218	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
vg0616479820	NA	3.52E-06	mr1526	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
vg0616479820	NA	6.40E-08	mr1218_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
vg0616479820	NA	2.28E-09	mr1530_2	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
vg0616479820	NA	9.70E-06	mr1734_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
vg0616479820	NA	7.86E-06	mr1745_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
vg0616479820	NA	8.00E-08	mr1850_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