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Detailed information for vg0114197089:

Variant ID: vg0114197089 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 14197089
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, T: 0.01, others allele: 0.00, population size: 93. )

Flanking Sequence (100 bp) in Reference Genome:

AATGACCTTTGACTTTCTTCCTTCGATTAGCTAGGGTGGCACAAGGATATATTGCTGTTGAGTTATATGTGACAGCTAGCGGTGAAATCATTATATATTT[C/T]
CATTATCTATACCAATATAAAAAGCACCAAGTTCATCCAACACCTCTCTCTCCTGACCCTTAGATCCGTTCATCCAACGGTTTATATCAAAAGTTAAATC

Reverse complement sequence

GATTTAACTTTTGATATAAACCGTTGGATGAACGGATCTAAGGGTCAGGAGAGAGAGGTGTTGGATGAACTTGGTGCTTTTTATATTGGTATAGATAATG[G/A]
AAATATATAATGATTTCACCGCTAGCTGTCACATATAACTCAACAGCAATATATCCTTGTGCCACCCTAGCTAATCGAAGGAAGAAAGTCAAAGGTCATT

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	65.30%	2.90%	0.59%	31.23%	NA
All Indica	2759	50.60%	2.70%	0.25%	46.50%	NA
All Japonica	1512	95.00%	3.60%	1.19%	0.13%	NA
Aus	269	37.90%	0.70%	0.37%	60.97%	NA
Indica I	595	49.60%	0.00%	0.00%	50.42%	NA
Indica II	465	21.50%	11.20%	0.86%	66.45%	NA
Indica III	913	67.60%	0.40%	0.00%	31.98%	NA
Indica Intermediate	786	48.70%	2.30%	0.38%	48.60%	NA
Temperate Japonica	767	91.40%	6.80%	1.83%	0.00%	NA
Tropical Japonica	504	99.40%	0.00%	0.40%	0.20%	NA
Japonica Intermediate	241	97.50%	1.20%	0.83%	0.41%	NA
VI/Aromatic	96	97.90%	0.00%	0.00%	2.08%	NA
Intermediate	90	63.30%	6.70%	2.22%	27.78%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0114197089	C -> T	LOC_Os01g25150-LOC_Os01g25160	intergenic_region ; MODIFIER	silent_mutation	Average:41.56; most accessible tissue: Callus, score: 91.374	N	N	N	N
vg0114197089	C -> DEL	N	N	silent_mutation	Average:41.56; most accessible tissue: Callus, score: 91.374	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0114197089	NA	2.83E-06	mr1296_2	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
vg0114197089	8.57E-07	8.57E-07	mr1452_2	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
vg0114197089	NA	6.94E-06	mr1712_2	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
vg0114197089	1.43E-06	4.64E-07	mr1761_2	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