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Detailed information for vg0421657372:

Variant ID: vg0421657372 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 21657372
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, T: 0.00, others allele: 0.00, population size: 272. )

Flanking Sequence (100 bp) in Reference Genome:

AAGCACAGCACGAGTTCCTTTGCTTGCCCTGCAGTTAATGTGAACCCTCTTTCTAAATCAAAGAAATGCACAGGCAGTAAATTTAGCTTCTGTGTGACGT[C/T]
GTTAACAAATAATGATAATTTAGCATCTTGGTAATTTTGTATGTATTTATACAGTGTCTGCTAATTTCTTTATATGAGTTTCAATGTTTTATTTTTATAT

Reverse complement sequence

ATATAAAAATAAAACATTGAAACTCATATAAAGAAATTAGCAGACACTGTATAAATACATACAAAATTACCAAGATGCTAAATTATCATTATTTGTTAAC[G/A]
ACGTCACACAGAAGCTAAATTTACTGCCTGTGCATTTCTTTGATTTAGAAAGAGGGTTCACATTAACTGCAGGGCAAGCAAAGGAACTCGTGCTGTGCTT

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	96.40%	2.10%	1.48%	0.00%	NA
All Indica	2759	99.20%	0.10%	0.76%	0.00%	NA
All Japonica	1512	91.70%	5.50%	2.78%	0.00%	NA
Aus	269	98.10%	0.40%	1.49%	0.00%	NA
Indica I	595	98.30%	0.00%	1.68%	0.00%	NA
Indica II	465	99.60%	0.00%	0.43%	0.00%	NA
Indica III	913	99.80%	0.10%	0.11%	0.00%	NA
Indica Intermediate	786	98.90%	0.10%	1.02%	0.00%	NA
Temperate Japonica	767	90.50%	5.10%	4.43%	0.00%	NA
Tropical Japonica	504	99.20%	0.40%	0.40%	0.00%	NA
Japonica Intermediate	241	80.10%	17.40%	2.49%	0.00%	NA
VI/Aromatic	96	89.60%	10.40%	0.00%	0.00%	NA
Intermediate	90	94.40%	2.20%	3.33%	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
vg0421657372	C -> T	LOC_Os04g35550.1	downstream_gene_variant ; 3952.0bp to feature; MODIFIER	silent_mutation	Average:50.812; most accessible tissue: Callus, score: 70.212	N	N	N	N
vg0421657372	C -> T	LOC_Os04g35560.1	downstream_gene_variant ; 4706.0bp to feature; MODIFIER	silent_mutation	Average:50.812; most accessible tissue: Callus, score: 70.212	N	N	N	N
vg0421657372	C -> T	LOC_Os04g35560.2	downstream_gene_variant ; 4706.0bp to feature; MODIFIER	silent_mutation	Average:50.812; most accessible tissue: Callus, score: 70.212	N	N	N	N
vg0421657372	C -> T	LOC_Os04g35540-LOC_Os04g35550	intergenic_region ; MODIFIER	silent_mutation	Average:50.812; most accessible tissue: Callus, score: 70.212	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0421657372	8.01E-08	8.01E-08	mr1191_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