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Detailed information for vg0622463232:

Variant ID: vg0622463232 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 22463232
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.74, T: 0.26, others allele: 0.00, population size: 73. )

Flanking Sequence (100 bp) in Reference Genome:

AGCTGGGCGGCAGGCCTTTTATAGGCAGCGAGGCCTGCCGCCCGGCCAGAGGGCGGCAAGGGGCCGCATGCAAAATGACCGGCCCCGACTGGCTTTTTTG[T/C]
ATTCGGACCCCTTGCCGCCCCACCAGAGGGCGGCAAGGGTTTTCCTACAAAAAACCCTCCCTCCGTCACTGCCCATTCCTCCCCCGTTTGCCACGTCAGC

Reverse complement sequence

GCTGACGTGGCAAACGGGGGAGGAATGGGCAGTGACGGAGGGAGGGTTTTTTGTAGGAAAACCCTTGCCGCCCTCTGGTGGGGCGGCAAGGGGTCCGAAT[A/G]
CAAAAAAGCCAGTCGGGGCCGGTCATTTTGCATGCGGCCCCTTGCCGCCCTCTGGCCGGGCGGCAGGCCTCGCTGCCTATAAAAGGCCTGCCGCCCAGCT

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	25.20%	17.70%	17.18%	39.86%	NA
All Indica	2759	6.00%	7.90%	23.56%	62.56%	NA
All Japonica	1512	59.90%	37.20%	0.20%	2.65%	NA
Aus	269	11.90%	10.00%	49.07%	29.00%	NA
Indica I	595	0.50%	1.30%	13.45%	84.71%	NA
Indica II	465	1.50%	12.30%	13.55%	72.69%	NA
Indica III	913	14.10%	8.40%	36.80%	40.64%	NA
Indica Intermediate	786	3.40%	9.50%	21.76%	65.27%	NA
Temperate Japonica	767	52.30%	46.00%	0.26%	1.43%	NA
Tropical Japonica	504	59.10%	35.90%	0.20%	4.76%	NA
Japonica Intermediate	241	85.90%	12.00%	0.00%	2.07%	NA
VI/Aromatic	96	64.60%	8.30%	17.71%	9.38%	NA
Intermediate	90	30.00%	24.40%	11.11%	34.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0622463232	T -> C	LOC_Os06g37970.1	upstream_gene_variant ; 605.0bp to feature; MODIFIER	silent_mutation	Average:45.458; most accessible tissue: Callus, score: 85.276	N	N	N	N
vg0622463232	T -> C	LOC_Os06g37990.1	upstream_gene_variant ; 3246.0bp to feature; MODIFIER	silent_mutation	Average:45.458; most accessible tissue: Callus, score: 85.276	N	N	N	N
vg0622463232	T -> C	LOC_Os06g37980.1	downstream_gene_variant ; 918.0bp to feature; MODIFIER	silent_mutation	Average:45.458; most accessible tissue: Callus, score: 85.276	N	N	N	N
vg0622463232	T -> C	LOC_Os06g37970-LOC_Os06g37980	intergenic_region ; MODIFIER	silent_mutation	Average:45.458; most accessible tissue: Callus, score: 85.276	N	N	N	N
vg0622463232	T -> DEL	N	N	silent_mutation	Average:45.458; most accessible tissue: Callus, score: 85.276	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0622463232	7.12E-07	NA	mr1136	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
vg0622463232	NA	6.32E-07	mr1136	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
vg0622463232	9.09E-06	9.09E-06	mr1465	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
vg0622463232	NA	2.77E-07	mr1662	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