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Detailed information for vg0421558945:

Variant ID: vg0421558945 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 21558945
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.93, T: 0.07, others allele: 0.00, population size: 116. )

Flanking Sequence (100 bp) in Reference Genome:

TGACTGCTTTTTTTTACAGGATCTGAGCTGAAATCCTGCAAAATTCATGCAAGAGTCATGCAAGAGAAGCATTGCTCGGACCCTGTTTAGATGGGACTAT[C/T]
CCTATCACATCGGATGTTTGGAAATTAATTATAAATATTAAACGTAGACTATTAATAAAACACATCCATAATTTTGGACTAATTCGCGAGACGAATCTAT

Reverse complement sequence

ATAGATTCGTCTCGCGAATTAGTCCAAAATTATGGATGTGTTTTATTAATAGTCTACGTTTAATATTTATAATTAATTTCCAAACATCCGATGTGATAGG[G/A]
ATAGTCCCATCTAAACAGGGTCCGAGCAATGCTTCTCTTGCATGACTCTTGCATGAATTTTGCAGGATTTCAGCTCAGATCCTGTAAAAAAAAGCAGTCA

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	58.00%	25.60%	0.78%	15.64%	NA
All Indica	2759	32.10%	40.30%	1.20%	26.42%	NA
All Japonica	1512	96.80%	3.00%	0.13%	0.07%	NA
Aus	269	91.40%	8.60%	0.00%	0.00%	NA
Indica I	595	31.90%	19.00%	1.34%	47.73%	NA
Indica II	465	6.70%	31.00%	2.15%	60.22%	NA
Indica III	913	38.80%	60.40%	0.33%	0.55%	NA
Indica Intermediate	786	39.60%	38.50%	1.53%	20.36%	NA
Temperate Japonica	767	99.70%	0.10%	0.13%	0.00%	NA
Tropical Japonica	504	91.70%	8.10%	0.00%	0.20%	NA
Japonica Intermediate	241	97.90%	1.70%	0.41%	0.00%	NA
VI/Aromatic	96	87.50%	12.50%	0.00%	0.00%	NA
Intermediate	90	70.00%	17.80%	2.22%	10.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0421558945	C -> DEL	N	N	silent_mutation	Average:49.166; most accessible tissue: Callus, score: 81.331	N	N	N	N
vg0421558945	C -> T	LOC_Os04g35420.1	upstream_gene_variant ; 630.0bp to feature; MODIFIER	silent_mutation	Average:49.166; most accessible tissue: Callus, score: 81.331	N	N	N	N
vg0421558945	C -> T	LOC_Os04g35430.1	downstream_gene_variant ; 284.0bp to feature; MODIFIER	silent_mutation	Average:49.166; most accessible tissue: Callus, score: 81.331	N	N	N	N
vg0421558945	C -> T	LOC_Os04g35420-LOC_Os04g35430	intergenic_region ; MODIFIER	silent_mutation	Average:49.166; most accessible tissue: Callus, score: 81.331	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0421558945	4.76E-06	NA	mr1304_2	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