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Detailed information for vg1217856333:

Variant ID: vg1217856333 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 17856333
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.97, T: 0.03, others allele: 0.00, population size: 101. )

Flanking Sequence (100 bp) in Reference Genome:

AGAATGATTTTTATTTCGGGATGAATTTATCAGGACGTGACAGATACACTGGAAGCACATAGTGATCTGAAGCATATGGAACAACGCGACGACCTTCACC[T/C]
GGAACCAAAGGAGAAAGGAAGCCATTACTTGAGTCCAGCCAGCTACACTCTTAGCAAGGCACAGAAGGAAAGTATGTTTGAATGCTTGAAGAGCATAAAG

Reverse complement sequence

CTTTATGCTCTTCAAGCATTCAAACATACTTTCCTTCTGTGCCTTGCTAAGAGTGTAGCTGGCTGGACTCAAGTAATGGCTTCCTTTCTCCTTTGGTTCC[A/G]
GGTGAAGGTCGTCGCGTTGTTCCATATGCTTCAGATCACTATGTGCTTCCAGTGTATCTGTCACGTCCTGATAAATTCATCCCGAAATAAAAATCATTCT

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	36.70%	24.10%	0.30%	38.95%	NA
All Indica	2759	41.40%	12.50%	0.47%	45.63%	NA
All Japonica	1512	27.00%	47.80%	0.00%	25.26%	NA
Aus	269	43.10%	10.00%	0.37%	46.47%	NA
Indica I	595	47.20%	6.60%	0.34%	45.88%	NA
Indica II	465	20.60%	29.20%	1.29%	48.82%	NA
Indica III	913	42.20%	7.80%	0.11%	49.95%	NA
Indica Intermediate	786	48.20%	12.70%	0.51%	38.55%	NA
Temperate Japonica	767	23.30%	74.20%	0.00%	2.48%	NA
Tropical Japonica	504	34.90%	11.70%	0.00%	53.37%	NA
Japonica Intermediate	241	22.00%	39.00%	0.00%	39.00%	NA
VI/Aromatic	96	35.40%	10.40%	0.00%	54.17%	NA
Intermediate	90	38.90%	35.60%	0.00%	25.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1217856333	T -> C	LOC_Os12g29860.1	missense_variant ; p.Leu66Pro; MODERATE	nonsynonymous_codon ; L66P	Average:16.787; most accessible tissue: Zhenshan97 flower, score: 28.855	unknown	unknown	TOLERATED	1.00
vg1217856333	T -> DEL	LOC_Os12g29860.1	N	frameshift_variant	Average:16.787; most accessible tissue: Zhenshan97 flower, score: 28.855	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1217856333	NA	3.30E-08	mr1826	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
vg1217856333	NA	6.14E-06	mr1332_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