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Detailed information for vg0100188252:

Variant ID: vg0100188252 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 188252
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: 304. )

Flanking Sequence (100 bp) in Reference Genome:

CTGAACAATTTGGAATGAATATGCAACTGTCCAAGTAAGATGTTGACCTATAGGGATATGGTGACTCACTGTGACTGAACAATTTGGAATGAATATGCAA[C/T]
TGTCAATTGAGATGTTGACCTATAGGGATGAATTGGAAAGAAGTACAGCAAGATGACTGAATTTACTGCAAAACTATGACTGAATTATAGAAGTTCATAA

Reverse complement sequence

TTATGAACTTCTATAATTCAGTCATAGTTTTGCAGTAAATTCAGTCATCTTGCTGTACTTCTTTCCAATTCATCCCTATAGGTCAACATCTCAATTGACA[G/A]
TTGCATATTCATTCCAAATTGTTCAGTCACAGTGAGTCACCATATCCCTATAGGTCAACATCTTACTTGGACAGTTGCATATTCATTCCAAATTGTTCAG

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	81.30%	18.70%	0.02%	0.00%	NA
All Indica	2759	70.70%	29.20%	0.04%	0.00%	NA
All Japonica	1512	97.70%	2.30%	0.00%	0.00%	NA
Aus	269	86.60%	13.40%	0.00%	0.00%	NA
Indica I	595	29.40%	70.60%	0.00%	0.00%	NA
Indica II	465	96.30%	3.70%	0.00%	0.00%	NA
Indica III	913	86.30%	13.60%	0.11%	0.00%	NA
Indica Intermediate	786	68.70%	31.30%	0.00%	0.00%	NA
Temperate Japonica	767	99.60%	0.40%	0.00%	0.00%	NA
Tropical Japonica	504	93.80%	6.20%	0.00%	0.00%	NA
Japonica Intermediate	241	99.60%	0.40%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	94.40%	5.60%	0.00%	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
vg0100188252	C -> T	LOC_Os01g01380.1	upstream_gene_variant ; 2784.0bp to feature; MODIFIER	silent_mutation	Average:52.975; most accessible tissue: Zhenshan97 root, score: 64.045	N	N	N	N
vg0100188252	C -> T	LOC_Os01g01369.1	intron_variant ; MODIFIER	silent_mutation	Average:52.975; most accessible tissue: Zhenshan97 root, score: 64.045	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0100188252	2.10E-06	NA	mr1718_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
vg0100188252	NA	4.55E-10	mr1739_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