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Detailed information for vg0112196285:

Variant ID: vg0112196285 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 12196285
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 241. )

Flanking Sequence (100 bp) in Reference Genome:

TCGACATGGCGGTCTGAAGATCTGACTCGTAGTCGACAACAGGGTAGCCTTCCTCCTCGAATCCGTGCCCGGCGAGATCAGAAATAGCGCTTTCGTCTCT[T/C]
CTAACAGTATCCGGAGACACCGTAGGGTACTAGCCGTGCTTATCCCTGAAGTCGATATCCGGCGGCGTGTCTTGGCGTATGTAGGCTTCTATGTTGATTG

Reverse complement sequence

CAATCAACATAGAAGCCTACATACGCCAAGACACGCCGCCGGATATCGACTTCAGGGATAAGCACGGCTAGTACCCTACGGTGTCTCCGGATACTGTTAG[A/G]
AGAGACGAAAGCGCTATTTCTGATCTCGCCGGGCACGGATTCGAGGAGGAAGGCTACCCTGTTGTCGACTACGAGTCAGATCTTCAGACCGCCATGTCGA

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	77.30%	17.30%	1.06%	4.36%	NA
All Indica	2759	97.60%	0.90%	1.20%	0.29%	NA
All Japonica	1512	35.30%	50.80%	1.12%	12.83%	NA
Aus	269	99.30%	0.70%	0.00%	0.00%	NA
Indica I	595	99.70%	0.30%	0.00%	0.00%	NA
Indica II	465	94.60%	2.40%	2.37%	0.65%	NA
Indica III	913	99.10%	0.10%	0.66%	0.11%	NA
Indica Intermediate	786	96.10%	1.40%	2.04%	0.51%	NA
Temperate Japonica	767	26.30%	62.70%	1.30%	9.65%	NA
Tropical Japonica	504	41.10%	35.70%	1.39%	21.83%	NA
Japonica Intermediate	241	51.50%	44.40%	0.00%	4.15%	NA
VI/Aromatic	96	99.00%	1.00%	0.00%	0.00%	NA
Intermediate	90	71.10%	24.40%	0.00%	4.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0112196285	T -> DEL	N	N	silent_mutation	Average:48.337; most accessible tissue: Minghui63 flag leaf, score: 66.004	N	N	N	N
vg0112196285	T -> C	LOC_Os01g21730.1	downstream_gene_variant ; 1953.0bp to feature; MODIFIER	silent_mutation	Average:48.337; most accessible tissue: Minghui63 flag leaf, score: 66.004	N	N	N	N
vg0112196285	T -> C	LOC_Os01g21720-LOC_Os01g21730	intergenic_region ; MODIFIER	silent_mutation	Average:48.337; most accessible tissue: Minghui63 flag leaf, score: 66.004	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0112196285	1.46E-06	NA	mr1705	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
vg0112196285	NA	2.07E-07	mr1330_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
vg0112196285	NA	8.36E-09	mr1576_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
vg0112196285	NA	3.02E-06	mr1977_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