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Detailed information for vg0804126025:

Variant ID: vg0804126025 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 4126025
Reference Allele: C	Alternative Allele: A
Primary Allele: C	Secondary Allele: A

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.98, A: 0.01, others allele: 0.00, population size: 236. )

Flanking Sequence (100 bp) in Reference Genome:

ACGCTAAATGTTTCACGCCTTGCAGGCCTCGAGTTCAGCCTTCATGTGTTGTAAAACCTTGCAGTTCGTTAGGGAGTGATTGGTTGTCTTGTGAATGACA[C/A]
ATCAAGCTGTAGATCTCTAAGGAGTTGTCCTCGTGGGTACTTGATTCCTAGTGGATAGGTGGGTTTTGGCCGCCTGAGGTCTTCTCCCATATGTTGTCAT

Reverse complement sequence

ATGACAACATATGGGAGAAGACCTCAGGCGGCCAAAACCCACCTATCCACTAGGAATCAAGTACCCACGAGGACAACTCCTTAGAGATCTACAGCTTGAT[G/T]
TGTCATTCACAAGACAACCAATCACTCCCTAACGAACTGCAAGGTTTTACAACACATGAAGGCTGAACTCGAGGCCTGCAAGGCGTGAAACATTTAGCGT

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	79.00%	2.30%	0.74%	17.90%	NA
All Indica	2759	66.60%	4.00%	1.05%	28.34%	NA
All Japonica	1512	96.30%	0.00%	0.33%	3.37%	NA
Aus	269	99.30%	0.00%	0.00%	0.74%	NA
Indica I	595	46.20%	3.50%	2.18%	48.07%	NA
Indica II	465	91.20%	1.70%	0.22%	6.88%	NA
Indica III	913	59.90%	6.40%	1.10%	32.64%	NA
Indica Intermediate	786	75.20%	3.10%	0.64%	21.12%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	89.10%	0.00%	0.99%	9.92%	NA
Japonica Intermediate	241	99.60%	0.00%	0.00%	0.41%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	86.70%	0.00%	1.11%	12.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0804126025	C -> A	LOC_Os08g07360.1	upstream_gene_variant ; 2379.0bp to feature; MODIFIER	silent_mutation	Average:40.313; most accessible tissue: Callus, score: 75.432	N	N	N	N
vg0804126025	C -> A	LOC_Os08g07370.1	downstream_gene_variant ; 1043.0bp to feature; MODIFIER	silent_mutation	Average:40.313; most accessible tissue: Callus, score: 75.432	N	N	N	N
vg0804126025	C -> A	LOC_Os08g07360-LOC_Os08g07370	intergenic_region ; MODIFIER	silent_mutation	Average:40.313; most accessible tissue: Callus, score: 75.432	N	N	N	N
vg0804126025	C -> DEL	N	N	silent_mutation	Average:40.313; most accessible tissue: Callus, score: 75.432	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0804126025	8.62E-07	8.59E-07	mr1340	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
vg0804126025	4.72E-06	4.72E-06	mr1340	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
vg0804126025	NA	5.26E-06	mr1347	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
vg0804126025	3.45E-06	NA	mr1709	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