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Detailed information for vg0124058988:

Variant ID: vg0124058988 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 24058988
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.63, C: 0.36, others allele: 0.00, population size: 104. )

Flanking Sequence (100 bp) in Reference Genome:

ACGCATGTTTTCAGAGAAATTTTAAGAAAATATCATTGATAAGCATCCCATTACACGTTTTGCCATCGAGAAATACCAGTTTAAAAGTAAAAATATACCA[T/C]
CATAGAATGGATGGATTCTAACCACGATGACATTCTAGCACAATGTAGCTCGCACGATGATATTTTCTATAAGTTGCGTCTGTTGATGACATTTTTTCAA

Reverse complement sequence

TTGAAAAAATGTCATCAACAGACGCAACTTATAGAAAATATCATCGTGCGAGCTACATTGTGCTAGAATGTCATCGTGGTTAGAATCCATCCATTCTATG[A/G]
TGGTATATTTTTACTTTTAAACTGGTATTTCTCGATGGCAAAACGTGTAATGGGATGCTTATCAATGATATTTTCTTAAAATTTCTCTGAAAACATGCGT

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	55.00%	44.90%	0.15%	0.00%	NA
All Indica	2759	42.50%	57.30%	0.22%	0.00%	NA
All Japonica	1512	84.90%	15.10%	0.00%	0.00%	NA
Aus	269	1.50%	98.50%	0.00%	0.00%	NA
Indica I	595	36.00%	64.00%	0.00%	0.00%	NA
Indica II	465	35.70%	63.70%	0.65%	0.00%	NA
Indica III	913	48.60%	51.30%	0.11%	0.00%	NA
Indica Intermediate	786	44.30%	55.50%	0.25%	0.00%	NA
Temperate Japonica	767	98.80%	1.20%	0.00%	0.00%	NA
Tropical Japonica	504	61.30%	38.70%	0.00%	0.00%	NA
Japonica Intermediate	241	90.00%	10.00%	0.00%	0.00%	NA
VI/Aromatic	96	88.50%	11.50%	0.00%	0.00%	NA
Intermediate	90	57.80%	41.10%	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
vg0124058988	T -> C	LOC_Os01g42350.1	upstream_gene_variant ; 3070.0bp to feature; MODIFIER	silent_mutation	Average:42.406; most accessible tissue: Callus, score: 76.237	N	N	N	N
vg0124058988	T -> C	LOC_Os01g42360.1	downstream_gene_variant ; 2274.0bp to feature; MODIFIER	silent_mutation	Average:42.406; most accessible tissue: Callus, score: 76.237	N	N	N	N
vg0124058988	T -> C	LOC_Os01g42350-LOC_Os01g42360	intergenic_region ; MODIFIER	silent_mutation	Average:42.406; most accessible tissue: Callus, score: 76.237	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0124058988	NA	2.79E-06	mr1082	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
vg0124058988	1.83E-06	NA	mr1090	Ind_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
vg0124058988	3.77E-07	NA	mr1096	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
vg0124058988	NA	4.79E-06	mr1207	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
vg0124058988	NA	2.03E-10	mr1307	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
vg0124058988	NA	2.12E-06	mr1622	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
vg0124058988	NA	6.70E-06	mr1633	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
vg0124058988	NA	4.96E-06	mr1787	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
vg0124058988	NA	3.51E-06	mr1906	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
vg0124058988	NA	4.72E-14	mr1921	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
vg0124058988	NA	1.88E-06	mr1960	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
vg0124058988	NA	4.86E-06	mr1082_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
vg0124058988	NA	4.64E-07	mr1495_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
vg0124058988	NA	4.19E-07	mr1653_2	Ind_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
vg0124058988	NA	8.69E-06	mr1936_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