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Detailed information for vg1226390556:

Variant ID: vg1226390556 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 26390556
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.95, T: 0.04, others allele: 0.00, population size: 103. )

Flanking Sequence (100 bp) in Reference Genome:

ATCACGCCCACCCTTGCCTGGATGCGTCAGCTAGAGGAAAGCTACACTACAAGCCCAGCCATTGCCCACGCTGGCTTGTGGTAAGTACGATGAATTCTTC[C/T]
AGGGTTTTCCGCGAACCGGTCCTTAATTGCCATGGGTGCGACTAGCAAAACCATGCACCCACAGCCCACCATTCAGTCGTATTTTAGTTGGATAATTACG

Reverse complement sequence

CGTAATTATCCAACTAAAATACGACTGAATGGTGGGCTGTGGGTGCATGGTTTTGCTAGTCGCACCCATGGCAATTAAGGACCGGTTCGCGGAAAACCCT[G/A]
GAAGAATTCATCGTACTTACCACAAGCCAGCGTGGGCAATGGCTGGGCTTGTAGTGTAGCTTTCCTCTAGCTGACGCATCCAGGCAAGGGTGGGCGTGAT

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	78.70%	20.30%	0.28%	0.78%	NA
All Indica	2759	63.90%	34.30%	0.47%	1.34%	NA
All Japonica	1512	99.70%	0.30%	0.00%	0.00%	NA
Aus	269	99.60%	0.40%	0.00%	0.00%	NA
Indica I	595	44.50%	55.50%	0.00%	0.00%	NA
Indica II	465	63.90%	31.00%	1.51%	3.66%	NA
Indica III	913	75.40%	22.60%	0.44%	1.64%	NA
Indica Intermediate	786	65.30%	33.80%	0.25%	0.64%	NA
Temperate Japonica	767	99.90%	0.10%	0.00%	0.00%	NA
Tropical Japonica	504	99.80%	0.20%	0.00%	0.00%	NA
Japonica Intermediate	241	99.20%	0.80%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	92.20%	7.80%	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
vg1226390556	C -> DEL	N	N	silent_mutation	Average:29.744; most accessible tissue: Zhenshan97 panicle, score: 65.386	N	N	N	N
vg1226390556	C -> T	LOC_Os12g42460.1	upstream_gene_variant ; 3139.0bp to feature; MODIFIER	silent_mutation	Average:29.744; most accessible tissue: Zhenshan97 panicle, score: 65.386	N	N	N	N
vg1226390556	C -> T	LOC_Os12g42470.1	upstream_gene_variant ; 2291.0bp to feature; MODIFIER	silent_mutation	Average:29.744; most accessible tissue: Zhenshan97 panicle, score: 65.386	N	N	N	N
vg1226390556	C -> T	LOC_Os12g42480.1	upstream_gene_variant ; 1052.0bp to feature; MODIFIER	silent_mutation	Average:29.744; most accessible tissue: Zhenshan97 panicle, score: 65.386	N	N	N	N
vg1226390556	C -> T	LOC_Os12g42470-LOC_Os12g42480	intergenic_region ; MODIFIER	silent_mutation	Average:29.744; most accessible tissue: Zhenshan97 panicle, score: 65.386	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1226390556	4.19E-06	2.68E-10	mr1575	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