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Detailed information for vg1217956699:

Variant ID: vg1217956699 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 17956699
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.70, T: 0.30, others allele: 0.00, population size: 241. )

Flanking Sequence (100 bp) in Reference Genome:

TCACTGGGGATAGGGCTTCGTTAGCCTGCAAACATAATATAAATCAATAATCGATTTAAATCTTTCTGTTTAACCAGGCGACCACCCTTGATTGGTGTAT[C/T]
AGGACCAATACGTACATAGACATTGGAATTGATCTAAAGTGATTTATGCTTTTGAATGAGGTTTGCATCTTAGGGAAGTAACGAGGGTTGCTGATTAAAT

Reverse complement sequence

ATTTAATCAGCAACCCTCGTTACTTCCCTAAGATGCAAACCTCATTCAAAAGCATAAATCACTTTAGATCAATTCCAATGTCTATGTACGTATTGGTCCT[G/A]
ATACACCAATCAAGGGTGGTCGCCTGGTTAAACAGAAAGATTTAAATCGATTATTGATTTATATTATGTTTGCAGGCTAACGAAGCCCTATCCCCAGTGA

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	52.50%	47.40%	0.11%	0.00%	NA
All Indica	2759	53.50%	46.40%	0.11%	0.00%	NA
All Japonica	1512	56.30%	43.70%	0.07%	0.00%	NA
Aus	269	26.80%	73.20%	0.00%	0.00%	NA
Indica I	595	39.70%	60.20%	0.17%	0.00%	NA
Indica II	465	61.10%	38.90%	0.00%	0.00%	NA
Indica III	913	57.90%	41.90%	0.11%	0.00%	NA
Indica Intermediate	786	54.50%	45.40%	0.13%	0.00%	NA
Temperate Japonica	767	72.00%	28.00%	0.00%	0.00%	NA
Tropical Japonica	504	27.80%	72.00%	0.20%	0.00%	NA
Japonica Intermediate	241	66.00%	34.00%	0.00%	0.00%	NA
VI/Aromatic	96	44.80%	55.20%	0.00%	0.00%	NA
Intermediate	90	43.30%	55.60%	1.11%	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
vg1217956699	C -> T	LOC_Os12g30020.1	intron_variant ; MODIFIER	silent_mutation	Average:64.849; most accessible tissue: Zhenshan97 flag leaf, score: 70.007	N	N	N	N
vg1217956699	C -> T	LOC_Os12g30020.2	intron_variant ; MODIFIER	silent_mutation	Average:64.849; most accessible tissue: Zhenshan97 flag leaf, score: 70.007	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1217956699	NA	2.96E-08	mr1271	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
vg1217956699	NA	9.30E-06	mr1903	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