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Detailed information for vg1209793056:

Variant ID: vg1209793056 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 9793056
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.64, T: 0.36, others allele: 0.00, population size: 88. )

Flanking Sequence (100 bp) in Reference Genome:

AGCCTTGCTCTATATCTCATCACCTCATTGTTTTCATTCTGTTTCTAGACGAAAACCCATTTGTATCCCACAGAAAAGATACCACGAGGAGTAGGCATTA[C/T]
AGCCGAGAATACATCTCTTTTGTAAAGCGAGGCTAATTCTGCGTCAATTGCGTCCTTCCATTTGTTCCAGTCAGAGCGCTTTTGGCACTCTTTTATAGAC

Reverse complement sequence

GTCTATAAAAGAGTGCCAAAAGCGCTCTGACTGGAACAAATGGAAGGACGCAATTGACGCAGAATTAGCCTCGCTTTACAAAAGAGATGTATTCTCGGCT[G/A]
TAATGCCTACTCCTCGTGGTATCTTTTCTGTGGGATACAAATGGGTTTTCGTCTAGAAACAGAATGAAAACAATGAGGTGATGAGATATAGAGCAAGGCT

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	79.40%	18.00%	1.16%	1.40%	NA
All Indica	2759	70.90%	27.50%	0.76%	0.83%	NA
All Japonica	1512	94.40%	4.20%	0.20%	1.19%	NA
Aus	269	77.70%	4.80%	8.18%	9.29%	NA
Indica I	595	82.90%	17.00%	0.00%	0.17%	NA
Indica II	465	57.00%	43.00%	0.00%	0.00%	NA
Indica III	913	70.40%	26.50%	1.86%	1.20%	NA
Indica Intermediate	786	70.50%	27.60%	0.51%	1.40%	NA
Temperate Japonica	767	96.10%	1.40%	0.13%	2.35%	NA
Tropical Japonica	504	96.60%	3.20%	0.20%	0.00%	NA
Japonica Intermediate	241	84.20%	15.40%	0.41%	0.00%	NA
VI/Aromatic	96	82.30%	11.50%	6.25%	0.00%	NA
Intermediate	90	92.20%	4.40%	3.33%	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
vg1209793056	C -> DEL	LOC_Os12g17100.1	N	frameshift_variant	Average:24.075; most accessible tissue: Minghui63 flag leaf, score: 35.078	N	N	N	N
vg1209793056	C -> T	LOC_Os12g17100.1	missense_variant ; p.Val496Ile; MODERATE	nonsynonymous_codon ; V496I	Average:24.075; most accessible tissue: Minghui63 flag leaf, score: 35.078	unknown	unknown	TOLERATED	0.16

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1209793056	NA	6.95E-06	mr1308_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
vg1209793056	4.27E-06	4.26E-06	mr1853_2	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