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Detailed information for vg0424198526:

Variant ID: vg0424198526 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 24198526
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.94, T: 0.06, others allele: 0.00, population size: 53. )

Flanking Sequence (100 bp) in Reference Genome:

CCATGACAGGAGAGGCCGAGAGGGAACAGTTAGTGACCAAAAGGAGTGAGAAATGCTCAGGGGTCTTCCGGCTAGCTCCACAAGGTGGTGGGCTAGACGA[C/T]
CTGGGTTCAAAGCCTCACCCCTTCTAATTATTTGATATTATGTCCTTCCCTAATATTCGAGTTTTTTTTTAGTGACCAAAAGGAGAAGGAACAGTTTTTT

Reverse complement sequence

AAAAAACTGTTCCTTCTCCTTTTGGTCACTAAAAAAAAACTCGAATATTAGGGAAGGACATAATATCAAATAATTAGAAGGGGTGAGGCTTTGAACCCAG[G/A]
TCGTCTAGCCCACCACCTTGTGGAGCTAGCCGGAAGACCCCTGAGCATTTCTCACTCCTTTTGGTCACTAACTGTTCCCTCTCGGCCTCTCCTGTCATGG

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	90.10%	2.10%	3.39%	4.49%	NA
All Indica	2759	90.20%	0.00%	3.81%	6.02%	NA
All Japonica	1512	91.10%	6.50%	2.45%	0.00%	NA
Aus	269	78.10%	0.00%	5.58%	16.36%	NA
Indica I	595	81.50%	0.00%	6.89%	11.60%	NA
Indica II	465	96.60%	0.00%	1.51%	1.94%	NA
Indica III	913	91.50%	0.00%	2.19%	6.35%	NA
Indica Intermediate	786	91.50%	0.00%	4.71%	3.82%	NA
Temperate Japonica	767	82.80%	12.50%	4.69%	0.00%	NA
Tropical Japonica	504	99.80%	0.20%	0.00%	0.00%	NA
Japonica Intermediate	241	99.20%	0.40%	0.41%	0.00%	NA
VI/Aromatic	96	99.00%	0.00%	1.04%	0.00%	NA
Intermediate	90	95.60%	0.00%	2.22%	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
vg0424198526	C -> DEL	N	N	silent_mutation	Average:55.105; most accessible tissue: Minghui63 root, score: 75.155	N	N	N	N
vg0424198526	C -> T	LOC_Os04g40770.1	downstream_gene_variant ; 3176.0bp to feature; MODIFIER	silent_mutation	Average:55.105; most accessible tissue: Minghui63 root, score: 75.155	N	N	N	N
vg0424198526	C -> T	LOC_Os04g40780.1	downstream_gene_variant ; 598.0bp to feature; MODIFIER	silent_mutation	Average:55.105; most accessible tissue: Minghui63 root, score: 75.155	N	N	N	N
vg0424198526	C -> T	LOC_Os04g40790.1	downstream_gene_variant ; 3787.0bp to feature; MODIFIER	silent_mutation	Average:55.105; most accessible tissue: Minghui63 root, score: 75.155	N	N	N	N
vg0424198526	C -> T	LOC_Os04g40770-LOC_Os04g40780	intergenic_region ; MODIFIER	silent_mutation	Average:55.105; most accessible tissue: Minghui63 root, score: 75.155	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0424198526	2.95E-06	2.95E-06	mr1973_2	Jap_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