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Detailed information for vg0115927407:

Variant ID: vg0115927407 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 15927407
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.01, others allele: 0.00, population size: 90. )

Flanking Sequence (100 bp) in Reference Genome:

TCAAATAGTCATATATGCGTAGTCTAACTGTCGTATATTAGAACCCTACACAATCTTATATGCTAAGTCTTGTTACAAATCTAATAATCTTATATTAAAA[C/T]
TAAGTCTAAGTGTCATATATTAAATCTAATAGTCTTAATTGCATTACAAATATAACAATAATATATATAATTACGTCACTTGCCTGCGCGAATTCCTTCG

Reverse complement sequence

CGAAGGAATTCGCGCAGGCAAGTGACGTAATTATATATATTATTGTTATATTTGTAATGCAATTAAGACTATTAGATTTAATATATGACACTTAGACTTA[G/A]
TTTTAATATAAGATTATTAGATTTGTAACAAGACTTAGCATATAAGATTGTGTAGGGTTCTAATATACGACAGTTAGACTACGCATATATGACTATTTGA

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	61.70%	0.40%	6.43%	31.53%	NA
All Indica	2759	41.20%	0.60%	9.50%	48.68%	NA
All Japonica	1512	97.50%	0.00%	0.00%	2.51%	NA
Aus	269	55.00%	0.70%	14.13%	30.11%	NA
Indica I	595	28.40%	0.80%	4.54%	66.22%	NA
Indica II	465	42.60%	0.20%	8.39%	48.82%	NA
Indica III	913	46.70%	0.90%	13.14%	39.32%	NA
Indica Intermediate	786	43.90%	0.30%	9.67%	46.18%	NA
Temperate Japonica	767	99.00%	0.00%	0.00%	1.04%	NA
Tropical Japonica	504	94.60%	0.00%	0.00%	5.36%	NA
Japonica Intermediate	241	98.80%	0.00%	0.00%	1.24%	NA
VI/Aromatic	96	95.80%	0.00%	0.00%	4.17%	NA
Intermediate	90	68.90%	0.00%	4.44%	26.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0115927407	C -> T	LOC_Os01g28420.1	upstream_gene_variant ; 836.0bp to feature; MODIFIER	silent_mutation	Average:15.25; most accessible tissue: Minghui63 panicle, score: 20.733	N	N	N	N
vg0115927407	C -> T	LOC_Os01g28440.1	downstream_gene_variant ; 1856.0bp to feature; MODIFIER	silent_mutation	Average:15.25; most accessible tissue: Minghui63 panicle, score: 20.733	N	N	N	N
vg0115927407	C -> T	LOC_Os01g28420-LOC_Os01g28440	intergenic_region ; MODIFIER	silent_mutation	Average:15.25; most accessible tissue: Minghui63 panicle, score: 20.733	N	N	N	N
vg0115927407	C -> DEL	N	N	silent_mutation	Average:15.25; most accessible tissue: Minghui63 panicle, score: 20.733	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0115927407	NA	6.16E-06	mr1419_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
vg0115927407	1.45E-06	1.45E-06	mr1727_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