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Detailed information for vg1226867292:

Variant ID: vg1226867292 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 26867292
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ATTTCTGGACGACGACGAGTGGATTCGAATACTTTTAAAGGGGATCCAGATCTCCGGTCATTGTTGGCGTCTTGTCCGCGAGGGTTGTCTGCTTGGGTTT[C/T]
GACTTCTGGAATCTCTTGGCTTGGCCCTACGTCCGACTGGTTTCCAGTCGGGGGCTCCTGATTAACTCCGGCTTTGGCTTCGGCCGACTGGATTCCAGTC

Reverse complement sequence

GACTGGAATCCAGTCGGCCGAAGCCAAAGCCGGAGTTAATCAGGAGCCCCCGACTGGAAACCAGTCGGACGTAGGGCCAAGCCAAGAGATTCCAGAAGTC[G/A]
AAACCCAAGCAGACAACCCTCGCGGACAAGACGCCAACAATGACCGGAGATCTGGATCCCCTTTAAAAGTATTCGAATCCACTCGTCGTCGTCCAGAAAT

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	90.40%	4.20%	4.19%	1.29%	NA
All Indica	2759	86.00%	5.50%	6.42%	2.14%	NA
All Japonica	1512	99.90%	0.00%	0.07%	0.00%	NA
Aus	269	79.90%	14.90%	5.20%	0.00%	NA
Indica I	595	92.80%	2.90%	3.53%	0.84%	NA
Indica II	465	81.90%	8.60%	9.03%	0.43%	NA
Indica III	913	83.90%	4.90%	6.90%	4.27%	NA
Indica Intermediate	786	85.60%	6.20%	6.49%	1.65%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	99.80%	0.00%	0.20%	0.00%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	96.90%	1.00%	1.04%	1.04%	NA
Intermediate	90	87.80%	5.60%	5.56%	1.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1226867292	C -> DEL	LOC_Os12g43280.1	N	frameshift_variant	Average:28.132; most accessible tissue: Zhenshan97 flag leaf, score: 65.82	N	N	N	N
vg1226867292	C -> T	LOC_Os12g43280.1	missense_variant ; p.Glu419Lys; MODERATE	nonsynonymous_codon ; E419K	Average:28.132; most accessible tissue: Zhenshan97 flag leaf, score: 65.82	unknown	unknown	DELETERIOUS	0.01

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1226867292	1.96E-06	NA	mr1131	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