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Detailed information for vg0624653755:

Variant ID: vg0624653755 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 24653755
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: 117. )

Flanking Sequence (100 bp) in Reference Genome:

CTCGCTCGACAACTTGCTTTTTTCTTGGGTACCCGGCCTCCCACAAGGGATACCGATGTCTGGATCTCTCCACTCGCCGCATCATCATTTCGCGCCACGT[C/T]
GTGTTTGACGAATCACGATTTCCCTTCGCAGCAACTCCCCCTGCTCCCTCGTCTTTTGATTTTTTGCTGCAGGGACTCCCTCCAGCGGTCGCTCCCTCAT

Reverse complement sequence

ATGAGGGAGCGACCGCTGGAGGGAGTCCCTGCAGCAAAAAATCAAAAGACGAGGGAGCAGGGGGAGTTGCTGCGAAGGGAAATCGTGATTCGTCAAACAC[G/A]
ACGTGGCGCGAAATGATGATGCGGCGAGTGGAGAGATCCAGACATCGGTATCCCTTGTGGGAGGCCGGGTACCCAAGAAAAAAGCAAGTTGTCGAGCGAG

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	48.90%	5.60%	1.69%	43.82%	NA
All Indica	2759	25.70%	7.00%	2.57%	64.70%	NA
All Japonica	1512	91.50%	0.00%	0.07%	8.40%	NA
Aus	269	30.50%	26.80%	2.97%	39.78%	NA
Indica I	595	6.40%	1.50%	1.68%	90.42%	NA
Indica II	465	12.00%	3.00%	1.94%	83.01%	NA
Indica III	913	44.20%	15.30%	3.18%	37.24%	NA
Indica Intermediate	786	27.00%	3.80%	2.93%	66.28%	NA
Temperate Japonica	767	97.90%	0.00%	0.00%	2.09%	NA
Tropical Japonica	504	78.80%	0.00%	0.20%	21.03%	NA
Japonica Intermediate	241	97.90%	0.00%	0.00%	2.07%	NA
VI/Aromatic	96	87.50%	0.00%	0.00%	12.50%	NA
Intermediate	90	54.40%	1.10%	0.00%	44.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0624653755	C -> T	LOC_Os06g41200.1	synonymous_variant ; p.Val111Val; LOW	synonymous_codon	Average:5.833; most accessible tissue: Callus, score: 16.518	N	N	N	N
vg0624653755	C -> DEL	LOC_Os06g41200.1	N	frameshift_variant	Average:5.833; most accessible tissue: Callus, score: 16.518	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0624653755	2.88E-06	4.97E-08	mr1812	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
vg0624653755	NA	1.97E-09	mr1322_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
vg0624653755	NA	1.56E-07	mr1527_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
vg0624653755	NA	6.03E-07	mr1623_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
vg0624653755	NA	2.76E-08	mr1690_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