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Detailed information for vg1214083827:

Variant ID: vg1214083827 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 14083827
Reference Allele: C	Alternative Allele: A
Primary Allele: C	Secondary Allele: A

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, A: 0.01, others allele: 0.00, population size: 111. )

Flanking Sequence (100 bp) in Reference Genome:

GCCTTTCTCAACGGACCTATCTCGGAGTTGGTCTATGTGGAGCAACCACCGGAGTTTGAGGATCCAAAGTTGCCAAACCATGTGTACAAGCTCCATAAGG[C/A]
GCTCTACGGGCTCAAACAAGCCCCTAGAGCTTGGTATGAATGTCTCTGAGATTTTCTTTTGAAAAATGGTTTTGAAATTGGAAAGGCGGATACTACTCTC

Reverse complement sequence

GAGAGTAGTATCCGCCTTTCCAATTTCAAAACCATTTTTCAAAAGAAAATCTCAGAGACATTCATACCAAGCTCTAGGGGCTTGTTTGAGCCCGTAGAGC[G/T]
CCTTATGGAGCTTGTACACATGGTTTGGCAACTTTGGATCCTCAAACTCCGGTGGTTGCTCCACATAGACCAACTCCGAGATAGGTCCGTTGAGAAAGGC

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	75.50%	15.60%	8.89%	0.04%	NA
All Indica	2759	59.20%	25.90%	14.86%	0.07%	NA
All Japonica	1512	99.40%	0.20%	0.40%	0.00%	NA
Aus	269	99.60%	0.40%	0.00%	0.00%	NA
Indica I	595	46.60%	10.10%	43.03%	0.34%	NA
Indica II	465	76.30%	19.80%	3.87%	0.00%	NA
Indica III	913	53.60%	42.60%	3.83%	0.00%	NA
Indica Intermediate	786	65.00%	22.10%	12.85%	0.00%	NA
Temperate Japonica	767	99.70%	0.00%	0.26%	0.00%	NA
Tropical Japonica	504	99.00%	0.60%	0.40%	0.00%	NA
Japonica Intermediate	241	99.20%	0.00%	0.83%	0.00%	NA
VI/Aromatic	96	87.50%	12.50%	0.00%	0.00%	NA
Intermediate	90	90.00%	5.60%	4.44%	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
vg1214083827	C -> DEL	LOC_Os12g24610.1	N	frameshift_variant	Average:21.913; most accessible tissue: Zhenshan97 flag leaf, score: 36.135	N	N	N	N
vg1214083827	C -> A	LOC_Os12g24610.1	missense_variant ; p.Ala1395Glu; MODERATE	nonsynonymous_codon ; A1395E	Average:21.913; most accessible tissue: Zhenshan97 flag leaf, score: 36.135	possibly damaging	1.971	DELETERIOUS	0.00

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1214083827	NA	1.98E-06	mr1358_2	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
vg1214083827	2.75E-06	NA	mr1739_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