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Detailed information for vg0127027003:

Variant ID: vg0127027003 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 27027003
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.56, C: 0.44, others allele: 0.00, population size: 103. )

Flanking Sequence (100 bp) in Reference Genome:

AACAAGCAAGAACAAGATAAAAGCAATCTGATATTGCAAATAGGAATGAATACACACGATAAGTTGGGGTTCCGAAGAACAAGCAGACGGGCGGTCTAGC[T/C]
GACACGCGAGCTGCAAGCAAGTAGCAATGGCTAAACTTTAATCTAACAAAACCCAATAAACCCTGAAGGAGTACCTAGCTATATATAGGGGTGGGAGGAC

Reverse complement sequence

GTCCTCCCACCCCTATATATAGCTAGGTACTCCTTCAGGGTTTATTGGGTTTTGTTAGATTAAAGTTTAGCCATTGCTACTTGCTTGCAGCTCGCGTGTC[A/G]
GCTAGACCGCCCGTCTGCTTGTTCTTCGGAACCCCAACTTATCGTGTGTATTCATTCCTATTTGCAATATCAGATTGCTTTTATCTTGTTCTTGCTTGTT

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	61.70%	35.80%	1.57%	0.91%	NA
All Indica	2759	97.90%	1.60%	0.47%	0.11%	NA
All Japonica	1512	4.00%	95.80%	0.07%	0.13%	NA
Aus	269	45.00%	20.80%	21.19%	13.01%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	97.40%	2.40%	0.22%	0.00%	NA
Indica III	913	98.70%	0.70%	0.66%	0.00%	NA
Indica Intermediate	786	95.50%	3.30%	0.76%	0.38%	NA
Temperate Japonica	767	0.40%	99.60%	0.00%	0.00%	NA
Tropical Japonica	504	10.90%	89.10%	0.00%	0.00%	NA
Japonica Intermediate	241	0.80%	97.90%	0.41%	0.83%	NA
VI/Aromatic	96	4.20%	91.70%	3.12%	1.04%	NA
Intermediate	90	36.70%	61.10%	0.00%	2.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0127027003	T -> DEL	N	N	silent_mutation	Average:54.91; most accessible tissue: Zhenshan97 panicle, score: 77.482	N	N	N	N
vg0127027003	T -> C	LOC_Os01g47290.1	upstream_gene_variant ; 4776.0bp to feature; MODIFIER	silent_mutation	Average:54.91; most accessible tissue: Zhenshan97 panicle, score: 77.482	N	N	N	N
vg0127027003	T -> C	LOC_Os01g47280-LOC_Os01g47290	intergenic_region ; MODIFIER	silent_mutation	Average:54.91; most accessible tissue: Zhenshan97 panicle, score: 77.482	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0127027003	NA	3.23E-22	mr1416	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
vg0127027003	NA	1.71E-29	mr1922	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
vg0127027003	NA	1.51E-24	mr1024_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
vg0127027003	NA	1.92E-15	mr1040_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
vg0127027003	NA	3.35E-24	mr1233_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
vg0127027003	9.00E-07	1.41E-18	mr1416_2	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
vg0127027003	NA	1.55E-12	mr1770_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
vg0127027003	NA	1.24E-21	mr1922_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