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Detailed information for vg1218493508:

Variant ID: vg1218493508 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 18493508
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.96, C: 0.04, others allele: 0.00, population size: 55. )

Flanking Sequence (100 bp) in Reference Genome:

GCCTGAGGAGAACCACGCTCTGACACCATACTCACCCATGCTGTGTCATACAAGGACAGTGATAATTCAACTCCCTGCAGCTTCTTCCTTGTGTTAGCTT[T/C]
GAGTTCCTTGTTGTGCTGCAATATTACAACAGAATATTAAACTCAACCAAGGAATCAGATAATAAGAGATTAGATATACTAGGGTGTATCTCTAAATTAA

Reverse complement sequence

TTAATTTAGAGATACACCCTAGTATATCTAATCTCTTATTATCTGATTCCTTGGTTGAGTTTAATATTCTGTTGTAATATTGCAGCACAACAAGGAACTC[A/G]
AAGCTAACACAAGGAAGAAGCTGCAGGGAGTTGAATTATCACTGTCCTTGTATGACACAGCATGGGTGAGTATGGTGTCAGAGCGTGGTTCTCCTCAGGC

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	84.70%	15.20%	0.15%	0.00%	NA
All Indica	2759	76.40%	23.50%	0.18%	0.00%	NA
All Japonica	1512	99.10%	0.90%	0.00%	0.00%	NA
Aus	269	87.40%	12.60%	0.00%	0.00%	NA
Indica I	595	76.10%	23.50%	0.34%	0.00%	NA
Indica II	465	73.80%	26.20%	0.00%	0.00%	NA
Indica III	913	73.70%	26.10%	0.22%	0.00%	NA
Indica Intermediate	786	81.20%	18.70%	0.13%	0.00%	NA
Temperate Japonica	767	99.20%	0.80%	0.00%	0.00%	NA
Tropical Japonica	504	99.00%	1.00%	0.00%	0.00%	NA
Japonica Intermediate	241	98.80%	1.20%	0.00%	0.00%	NA
VI/Aromatic	96	86.50%	13.50%	0.00%	0.00%	NA
Intermediate	90	87.80%	10.00%	2.22%	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
vg1218493508	T -> C	LOC_Os12g30800.1	missense_variant ; p.Lys56Glu; MODERATE	nonsynonymous_codon ; K56E	Average:39.46; most accessible tissue: Callus, score: 61.407	unknown	unknown	TOLERATED	0.66

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1218493508	1.84E-06	NA	mr1457	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
vg1218493508	4.90E-06	1.79E-07	mr1457	Ind_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
vg1218493508	1.48E-09	NA	mr1458	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
vg1218493508	8.07E-08	1.26E-11	mr1458	Ind_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
vg1218493508	1.39E-06	NA	mr1457_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
vg1218493508	2.58E-06	7.10E-09	mr1457_2	Ind_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
vg1218493508	1.04E-09	NA	mr1458_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
vg1218493508	9.14E-10	1.24E-12	mr1458_2	Ind_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