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Detailed information for vg0111823078:

Variant ID: vg0111823078 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 11823078
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.92, T: 0.08, others allele: 0.00, population size: 107. )

Flanking Sequence (100 bp) in Reference Genome:

TCTCTAGGGACAACCATCTTTTTCCTTAACACACCGAACTTCATATTGCGACCGGTTGGACTTGGCAACCCAAAACTCTCTATGAAGTGACACTGCAAAA[C/T]
GTTTTACCTCCTCCTTCATATCTTCTGCTCTAGTATAAATCGCTCCCTGAATAACCTCATTTTCTTTGTACTCCCATCTCACACTATCCTCTTCAGAGAC

Reverse complement sequence

GTCTCTGAAGAGGATAGTGTGAGATGGGAGTACAAAGAAAATGAGGTTATTCAGGGAGCGATTTATACTAGAGCAGAAGATATGAAGGAGGAGGTAAAAC[G/A]
TTTTGCAGTGTCACTTCATAGAGAGTTTTGGGTTGCCAAGTCCAACCGGTCGCAATATGAAGTTCGGTGTGTTAAGGAAAAAGATGGTTGTCCCTAGAGA

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	34.30%	1.90%	18.28%	45.47%	NA
All Indica	2759	3.00%	3.20%	29.97%	63.79%	NA
All Japonica	1512	96.20%	0.00%	0.40%	3.44%	NA
Aus	269	8.90%	0.40%	7.06%	83.64%	NA
Indica I	595	2.40%	2.50%	18.49%	76.64%	NA
Indica II	465	4.50%	1.10%	12.69%	81.72%	NA
Indica III	913	1.90%	4.90%	46.00%	47.21%	NA
Indica Intermediate	786	3.90%	3.10%	30.28%	62.72%	NA
Temperate Japonica	767	97.80%	0.00%	0.52%	1.69%	NA
Tropical Japonica	504	93.30%	0.00%	0.40%	6.35%	NA
Japonica Intermediate	241	97.10%	0.00%	0.00%	2.90%	NA
VI/Aromatic	96	21.90%	0.00%	1.04%	77.08%	NA
Intermediate	90	43.30%	2.20%	12.22%	42.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0111823078	C -> T	LOC_Os01g21190.1	splice_region_variant&intron_variant ; LOW	silent_mutation	Average:11.684; most accessible tissue: Minghui63 root, score: 19.68	N	N	N	N
vg0111823078	C -> T	LOC_Os01g21200.1	downstream_gene_variant ; 2084.0bp to feature; MODIFIER	silent_mutation	Average:11.684; most accessible tissue: Minghui63 root, score: 19.68	N	N	N	N
vg0111823078	C -> DEL	N	N	silent_mutation	Average:11.684; most accessible tissue: Minghui63 root, score: 19.68	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0111823078	NA	1.13E-82	mr1672	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
vg0111823078	NA	1.37E-89	mr1758	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
vg0111823078	NA	1.91E-20	mr1838	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
vg0111823078	NA	1.11E-07	mr1335_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
vg0111823078	NA	9.39E-63	mr1733_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
vg0111823078	2.91E-07	NA	mr1758_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