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Detailed information for vg0505645439:

Variant ID: vg0505645439 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 5645439
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.95, T: 0.06, others allele: 0.00, population size: 245. )

Flanking Sequence (100 bp) in Reference Genome:

GTAAGATGGCCAGCCTATTTGACAAGTCAATAGAGAACGATCTTCCTCCAGAAGCACGAACTGGTGCACAAGTCTTCGACATGACAAAGAAGATTAAGGT[C/T]
GTGTTCGGGAAGGTAAAGAAGAAGGCAGTCAAGATGAAGAAAGCAAAGGATAAGGATGATACAGATGCGACGGATCAGGAAAATACATTGCCTTTCAAGA

Reverse complement sequence

TCTTGAAAGGCAATGTATTTTCCTGATCCGTCGCATCTGTATCATCCTTATCCTTTGCTTTCTTCATCTTGACTGCCTTCTTCTTTACCTTCCCGAACAC[G/A]
ACCTTAATCTTCTTTGTCATGTCGAAGACTTGTGCACCAGTTCGTGCTTCTGGAGGAAGATCGTTCTCTATTGACTTGTCAAATAGGCTGGCCATCTTAC

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	89.10%	7.20%	2.62%	1.10%	NA
All Indica	2759	92.10%	4.90%	2.17%	0.87%	NA
All Japonica	1512	93.70%	0.30%	4.17%	1.85%	NA
Aus	269	29.40%	70.60%	0.00%	0.00%	NA
Indica I	595	96.00%	0.20%	3.70%	0.17%	NA
Indica II	465	93.10%	3.40%	2.80%	0.65%	NA
Indica III	913	90.30%	6.90%	1.42%	1.42%	NA
Indica Intermediate	786	90.70%	6.90%	1.53%	0.89%	NA
Temperate Japonica	767	99.00%	0.00%	0.65%	0.39%	NA
Tropical Japonica	504	88.30%	0.20%	8.93%	2.58%	NA
Japonica Intermediate	241	88.40%	1.20%	5.39%	4.98%	NA
VI/Aromatic	96	92.70%	7.30%	0.00%	0.00%	NA
Intermediate	90	93.30%	5.60%	1.11%	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
vg0505645439	C -> T	LOC_Os05g10340.1	synonymous_variant ; p.Val370Val; LOW	synonymous_codon	Average:16.098; most accessible tissue: Callus, score: 53.107	N	N	N	N
vg0505645439	C -> DEL	LOC_Os05g10340.1	N	frameshift_variant	Average:16.098; most accessible tissue: Callus, score: 53.107	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0505645439	6.23E-08	5.37E-06	mr1697	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
vg0505645439	9.78E-11	2.52E-12	mr1697	Ind_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