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Detailed information for vg1205521566:

Variant ID: vg1205521566 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 5521566
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.02, others allele: 0.00, population size: 55. )

Flanking Sequence (100 bp) in Reference Genome:

TCTTCGGGTATAAATAGACCCCGAGCCATATGTAATTTTTAACACACGTTAAATACAATCTCGGCGCATCGCCATCCTTTTTGCTTTAGTTTTGTTTCGA[C/T]
GAGTTCTTGCTTTCGGGTTGAGCTGCATCGGTTTCGATCTTCATCAAGAGGTAAAATTCATTATGACGGATTGCGTTCTTAGGATTAGTGCTTCCATCCT

Reverse complement sequence

AGGATGGAAGCACTAATCCTAAGAACGCAATCCGTCATAATGAATTTTACCTCTTGATGAAGATCGAAACCGATGCAGCTCAACCCGAAAGCAAGAACTC[G/A]
TCGAAACAAAACTAAAGCAAAAAGGATGGCGATGCGCCGAGATTGTATTTAACGTGTGTTAAAAATTACATATGGCTCGGGGTCTATTTATACCCGAAGA

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	88.90%	2.30%	8.00%	0.72%	NA
All Indica	2759	83.50%	3.90%	12.14%	0.43%	NA
All Japonica	1512	99.90%	0.10%	0.07%	0.00%	NA
Aus	269	78.80%	0.00%	14.13%	7.06%	NA
Indica I	595	55.50%	9.10%	34.79%	0.67%	NA
Indica II	465	89.70%	4.70%	5.59%	0.00%	NA
Indica III	913	99.60%	0.10%	0.11%	0.22%	NA
Indica Intermediate	786	82.40%	3.90%	12.85%	0.76%	NA
Temperate Japonica	767	99.70%	0.10%	0.13%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	90.00%	2.20%	4.44%	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
vg1205521566	C -> DEL	N	N	silent_mutation	Average:14.491; most accessible tissue: Callus, score: 23.281	N	N	N	N
vg1205521566	C -> T	LOC_Os12g10420.1	upstream_gene_variant ; 1066.0bp to feature; MODIFIER	silent_mutation	Average:14.491; most accessible tissue: Callus, score: 23.281	N	N	N	N
vg1205521566	C -> T	LOC_Os12g10430.1	upstream_gene_variant ; 3315.0bp to feature; MODIFIER	silent_mutation	Average:14.491; most accessible tissue: Callus, score: 23.281	N	N	N	N
vg1205521566	C -> T	LOC_Os12g10410-LOC_Os12g10420	intergenic_region ; MODIFIER	silent_mutation	Average:14.491; most accessible tissue: Callus, score: 23.281	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1205521566	4.75E-06	NA	mr1241_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