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Detailed information for vg0814639996:

Variant ID: vg0814639996 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 14639996
Reference Allele: A	Alternative Allele: C
Primary Allele: C	Secondary Allele: A

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.01, others allele: 0.00, population size: 177. )

Flanking Sequence (100 bp) in Reference Genome:

GTACATCATAGAGCTCAAAGCTGGACTCATCCTGGTAGACCAGGGGAAGGTTGGTGCCCGAGGCATTCGTTAGAGTTTAACTTTAACATCCATAGGAGTC[A/C]
TCTCTAGCATGTCCTATCATCAGATGTTGTCCTTGGATAAAATCATGTTCTTAGATATACACACATGTTCCCTATGATTCAATACCCTTGGAATACTCTG

Reverse complement sequence

CAGAGTATTCCAAGGGTATTGAATCATAGGGAACATGTGTGTATATCTAAGAACATGATTTTATCCAAGGACAACATCTGATGATAGGACATGCTAGAGA[T/G]
GACTCCTATGGATGTTAAAGTTAAACTCTAACGAATGCCTCGGGCACCAACCTTCCCCTGGTCTACCAGGATGAGTCCAGCTTTGAGCTCTATGATGTAC

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	33.90%	6.10%	0.19%	59.84%	NA
All Indica	2759	11.10%	0.70%	0.18%	88.04%	NA
All Japonica	1512	76.70%	17.00%	0.07%	6.22%	NA
Aus	269	0.70%	0.00%	0.74%	98.51%	NA
Indica I	595	2.70%	0.70%	0.34%	96.30%	NA
Indica II	465	8.60%	1.30%	0.22%	89.89%	NA
Indica III	913	18.20%	0.10%	0.11%	81.60%	NA
Indica Intermediate	786	10.70%	1.00%	0.13%	88.17%	NA
Temperate Japonica	767	63.80%	31.30%	0.13%	4.82%	NA
Tropical Japonica	504	93.80%	0.40%	0.00%	5.75%	NA
Japonica Intermediate	241	82.20%	6.20%	0.00%	11.62%	NA
VI/Aromatic	96	95.80%	0.00%	0.00%	4.17%	NA
Intermediate	90	46.70%	12.20%	1.11%	40.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0814639996	A -> C	LOC_Os08g24260.1	upstream_gene_variant ; 2891.0bp to feature; MODIFIER	silent_mutation	Average:12.633; most accessible tissue: Callus, score: 79.478	N	N	N	N
vg0814639996	A -> C	LOC_Os08g24240.1	downstream_gene_variant ; 3865.0bp to feature; MODIFIER	silent_mutation	Average:12.633; most accessible tissue: Callus, score: 79.478	N	N	N	N
vg0814639996	A -> C	LOC_Os08g24250.1	intron_variant ; MODIFIER	silent_mutation	Average:12.633; most accessible tissue: Callus, score: 79.478	N	N	N	N
vg0814639996	A -> DEL	N	N	silent_mutation	Average:12.633; most accessible tissue: Callus, score: 79.478	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0814639996	2.30E-06	NA	mr1133_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
vg0814639996	9.03E-06	NA	mr1726_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