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Detailed information for vg0806613735:

Variant ID: vg0806613735 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 6613735
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.91, T: 0.09, others allele: 0.00, population size: 76. )

Flanking Sequence (100 bp) in Reference Genome:

TGATCTATGGCTGCATGTCTCTAGTTGTACATGAGTTGTACAACTGAGTCGTATATTTTTTTCTCCCATGGAAAGAAAGAAAGCAGCACCCCTCTCTCCT[T/C]
GTTTCCTTCTCCCGTGGACGCCTAAATGCTGCCGGTGAAAGCTGGCCGTGGTGGAGGAGCTAGAGGAGGTGGGAGTTCTTCTTATGCTACCGGTCCCACT

Reverse complement sequence

AGTGGGACCGGTAGCATAAGAAGAACTCCCACCTCCTCTAGCTCCTCCACCACGGCCAGCTTTCACCGGCAGCATTTAGGCGTCCACGGGAGAAGGAAAC[A/G]
AGGAGAGAGGGGTGCTGCTTTCTTTCTTTCCATGGGAGAAAAAAATATACGACTCAGTTGTACAACTCATGTACAACTAGAGACATGCAGCCATAGATCA

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	85.70%	0.30%	4.08%	9.90%	NA
All Indica	2759	77.80%	0.40%	5.15%	16.67%	NA
All Japonica	1512	97.20%	0.00%	2.65%	0.20%	NA
Aus	269	97.40%	0.00%	1.86%	0.74%	NA
Indica I	595	68.10%	0.30%	4.20%	27.39%	NA
Indica II	465	75.70%	1.10%	3.44%	19.78%	NA
Indica III	913	82.00%	0.20%	8.32%	9.42%	NA
Indica Intermediate	786	81.40%	0.30%	3.18%	15.14%	NA
Temperate Japonica	767	95.20%	0.00%	4.69%	0.13%	NA
Tropical Japonica	504	99.20%	0.00%	0.79%	0.00%	NA
Japonica Intermediate	241	99.20%	0.00%	0.00%	0.83%	NA
VI/Aromatic	96	91.70%	2.10%	6.25%	0.00%	NA
Intermediate	90	95.60%	1.10%	0.00%	3.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0806613735	T -> C	LOC_Os08g11250.1	upstream_gene_variant ; 489.0bp to feature; MODIFIER	silent_mutation	Average:29.715; most accessible tissue: Minghui63 panicle, score: 56.842	N	N	N	N
vg0806613735	T -> C	LOC_Os08g11240.1	downstream_gene_variant ; 4914.0bp to feature; MODIFIER	silent_mutation	Average:29.715; most accessible tissue: Minghui63 panicle, score: 56.842	N	N	N	N
vg0806613735	T -> C	LOC_Os08g11240-LOC_Os08g11250	intergenic_region ; MODIFIER	silent_mutation	Average:29.715; most accessible tissue: Minghui63 panicle, score: 56.842	N	N	N	N
vg0806613735	T -> DEL	N	N	silent_mutation	Average:29.715; most accessible tissue: Minghui63 panicle, score: 56.842	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0806613735	NA	3.81E-06	mr1648	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
vg0806613735	NA	9.51E-06	mr1851	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
vg0806613735	2.78E-06	2.77E-06	mr1848_2	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