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Detailed information for vg0626663016:

Variant ID: vg0626663016 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 26663016
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.98, T: 0.01, others allele: 0.00, population size: 241. )

Flanking Sequence (100 bp) in Reference Genome:

AATATTTGTTCAAATTTAACTAAATTTTGTTCAAAATTTCAGAAATTTCGGATCGAAATTTCCGAAATTTCGGCATTTCGGTGAGGCCCAATCAAATCGG[C/T]
CTAACCGATAGGATTAACCCTGGTGGTAAGTGGTATGTGTGTGTTGAGTAAAATCCTGTATTCAAGGCACCTTGATGGTGCTGTTCTACCGTTTCCTACC

Reverse complement sequence

GGTAGGAAACGGTAGAACAGCACCATCAAGGTGCCTTGAATACAGGATTTTACTCAACACACACATACCACTTACCACCAGGGTTAATCCTATCGGTTAG[G/A]
CCGATTTGATTGGGCCTCACCGAAATGCCGAAATTTCGGAAATTTCGATCCGAAATTTCTGAAATTTTGAACAAAATTTAGTTAAATTTGAACAAATATT

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	95.90%	4.00%	0.08%	0.00%	NA
All Indica	2759	99.50%	0.50%	0.04%	0.00%	NA
All Japonica	1512	96.60%	3.20%	0.20%	0.00%	NA
Aus	269	55.80%	44.20%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	98.90%	1.10%	0.00%	0.00%	NA
Indica III	913	99.80%	0.20%	0.00%	0.00%	NA
Indica Intermediate	786	99.10%	0.80%	0.13%	0.00%	NA
Temperate Japonica	767	97.00%	2.60%	0.39%	0.00%	NA
Tropical Japonica	504	94.60%	5.40%	0.00%	0.00%	NA
Japonica Intermediate	241	99.60%	0.40%	0.00%	0.00%	NA
VI/Aromatic	96	97.90%	2.10%	0.00%	0.00%	NA
Intermediate	90	91.10%	8.90%	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
vg0626663016	C -> T	LOC_Os06g44180.1	upstream_gene_variant ; 3753.0bp to feature; MODIFIER	silent_mutation	Average:56.408; most accessible tissue: Callus, score: 72.144	N	N	N	N
vg0626663016	C -> T	LOC_Os06g44190.1	downstream_gene_variant ; 2659.0bp to feature; MODIFIER	silent_mutation	Average:56.408; most accessible tissue: Callus, score: 72.144	N	N	N	N
vg0626663016	C -> T	LOC_Os06g44210.1	downstream_gene_variant ; 2129.0bp to feature; MODIFIER	silent_mutation	Average:56.408; most accessible tissue: Callus, score: 72.144	N	N	N	N
vg0626663016	C -> T	LOC_Os06g44210.2	downstream_gene_variant ; 2129.0bp to feature; MODIFIER	silent_mutation	Average:56.408; most accessible tissue: Callus, score: 72.144	N	N	N	N
vg0626663016	C -> T	LOC_Os06g44200.1	intron_variant ; MODIFIER	silent_mutation	Average:56.408; most accessible tissue: Callus, score: 72.144	N	N	N	N
vg0626663016	C -> T	LOC_Os06g44200.2	intron_variant ; MODIFIER	silent_mutation	Average:56.408; most accessible tissue: Callus, score: 72.144	N	N	N	N
vg0626663016	C -> T	LOC_Os06g44200.3	intron_variant ; MODIFIER	silent_mutation	Average:56.408; most accessible tissue: Callus, score: 72.144	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0626663016	8.93E-06	NA	mr1549	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
vg0626663016	6.12E-08	NA	mr1757	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