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Detailed information for vg1218458718:

Variant ID: vg1218458718 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 18458718
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.76, T: 0.22, others allele: 0.00, population size: 41. )

Flanking Sequence (100 bp) in Reference Genome:

GAATGAGCTCCTCGGCAGCGACAACGATGAGCTTGATGCCTACTGGCCTCTCCTCAATTCGGCACTGCCGGCTATCAATTTGATGGGGCGGCGCCTCGAA[C/T]
AGAAGGCTAAGGAGGGAGCAGAAGGAGGTCCAGGAGAGGCACATTCGATGGCCAGAGGAGGAGGTGGAGCCGGTGGTCTCGATCAGAGTGGCTCCGTCGA

Reverse complement sequence

TCGACGGAGCCACTCTGATCGAGACCACCGGCTCCACCTCCTCCTCTGGCCATCGAATGTGCCTCTCCTGGACCTCCTTCTGCTCCCTCCTTAGCCTTCT[G/A]
TTCGAGGCGCCGCCCCATCAAATTGATAGCCGGCAGTGCCGAATTGAGGAGAGGCCAGTAGGCATCAAGCTCATCGTTGTCGCTGCCGAGGAGCTCATTC

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	80.00%	10.10%	1.06%	8.84%	NA
All Indica	2759	67.60%	16.50%	1.63%	14.35%	NA
All Japonica	1512	99.20%	0.40%	0.00%	0.40%	NA
Aus	269	95.50%	1.90%	0.00%	2.60%	NA
Indica I	595	46.10%	34.50%	2.02%	17.48%	NA
Indica II	465	82.40%	8.40%	1.08%	8.17%	NA
Indica III	913	72.40%	8.20%	1.97%	17.42%	NA
Indica Intermediate	786	69.50%	17.20%	1.27%	12.09%	NA
Temperate Japonica	767	99.20%	0.40%	0.00%	0.39%	NA
Tropical Japonica	504	99.20%	0.40%	0.00%	0.40%	NA
Japonica Intermediate	241	99.20%	0.40%	0.00%	0.41%	NA
VI/Aromatic	96	87.50%	6.20%	0.00%	6.25%	NA
Intermediate	90	84.40%	6.70%	5.56%	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
vg1218458718	C -> DEL	LOC_Os12g30730.1	N	frameshift_variant	Average:36.904; most accessible tissue: Callus, score: 58.641	N	N	N	N
vg1218458718	C -> T	LOC_Os12g30730.1	synonymous_variant ; p.Leu59Leu; LOW	synonymous_codon	Average:36.904; most accessible tissue: Callus, score: 58.641	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1218458718	1.71E-06	1.71E-06	mr1193	Jap_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
vg1218458718	NA	1.27E-06	mr1321	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