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Detailed information for vg1215059927:

Variant ID: vg1215059927 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 15059927
Reference Allele: C	Alternative Allele: T,A
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 92. )

Flanking Sequence (100 bp) in Reference Genome:

GCTACTGGACATCCTCGACATCAACATCTCTACAAACGACAACAAAGTTCTCAAGATCAAAATGCTGAAAACGCTAAGGTGATGACTGCGCACACAAAGG[C/T,A]
GGTTGGAACCAATAAAAGTTTTACAAAGCATGGCCAAAGAGTACAAGAGAGCTAAGACCCTACTCTTCAAAAAGAGGGAGGACGGACTCTCCCAGGTCAC

Reverse complement sequence

GTGACCTGGGAGAGTCCGTCCTCCCTCTTTTTGAAGAGTAGGGTCTTAGCTCTCTTGTACTCTTTGGCCATGCTTTGTAAAACTTTTATTGGTTCCAACC[G/A,T]
CCTTTGTGTGCGCAGTCATCACCTTAGCGTTTTCAGCATTTTGATCTTGAGAACTTTGTTGTCGTTTGTAGAGATGTTGATGTCGAGGATGTCCAGTAGC

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	73.40%	12.70%	8.95%	4.82%	A: 0.13%
All Indica	2759	65.60%	12.70%	13.85%	7.87%	NA
All Japonica	1512	82.00%	15.50%	1.92%	0.53%	NA
Aus	269	95.20%	1.10%	1.49%	0.00%	A: 2.23%
Indica I	595	59.50%	3.40%	10.76%	26.39%	NA
Indica II	465	61.70%	15.70%	20.86%	1.72%	NA
Indica III	913	71.70%	14.10%	13.69%	0.44%	NA
Indica Intermediate	786	65.40%	16.30%	12.21%	6.11%	NA
Temperate Japonica	767	91.50%	7.20%	1.17%	0.13%	NA
Tropical Japonica	504	70.20%	26.40%	2.38%	0.99%	NA
Japonica Intermediate	241	76.30%	19.50%	3.32%	0.83%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	76.70%	11.10%	8.89%	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
vg1215059927	C -> DEL	N	N	silent_mutation	Average:25.327; most accessible tissue: Minghui63 panicle, score: 53.77	N	N	N	N
vg1215059927	C -> A	LOC_Os12g25940.1	intron_variant ; MODIFIER	silent_mutation	Average:25.327; most accessible tissue: Minghui63 panicle, score: 53.77	N	N	N	N
vg1215059927	C -> T	LOC_Os12g25940.1	intron_variant ; MODIFIER	silent_mutation	Average:25.327; most accessible tissue: Minghui63 panicle, score: 53.77	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1215059927	4.96E-07	2.96E-07	mr1120	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
vg1215059927	NA	7.64E-07	mr1623_2	Jap_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