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Detailed information for vg0413703292:

Variant ID: vg0413703292 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 13703292
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, T: 0.02, others allele: 0.00, population size: 209. )

Flanking Sequence (100 bp) in Reference Genome:

ACATAGCACAGACGCAAGAATGGTAACAAACTGCTGATGCTCAGTTCGCCAACTTCACCAACATGATGCAGCAATAGCATGATGACCTTCAAGCGTACTT[C/T]
CGCTTCTAGGGGTTCAATCCTTATCAAGGACCTTGAGCGAAAGACAAGCTTGGGGGGAGACTCCCCCCACTGAGGTAACTTGTATCACATTGCATATTTC

Reverse complement sequence

GAAATATGCAATGTGATACAAGTTACCTCAGTGGGGGGAGTCTCCCCCCAAGCTTGTCTTTCGCTCAAGGTCCTTGATAAGGATTGAACCCCTAGAAGCG[G/A]
AAGTACGCTTGAAGGTCATCATGCTATTGCTGCATCATGTTGGTGAAGTTGGCGAACTGAGCATCAGCAGTTTGTTACCATTCTTGCGTCTGTGCTATGT

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	51.40%	48.50%	0.11%	0.00%	NA
All Indica	2759	34.10%	65.70%	0.18%	0.00%	NA
All Japonica	1512	92.10%	7.90%	0.00%	0.00%	NA
Aus	269	5.20%	94.80%	0.00%	0.00%	NA
Indica I	595	52.60%	47.40%	0.00%	0.00%	NA
Indica II	465	27.10%	72.70%	0.22%	0.00%	NA
Indica III	913	20.70%	79.10%	0.22%	0.00%	NA
Indica Intermediate	786	39.80%	59.90%	0.25%	0.00%	NA
Temperate Japonica	767	98.80%	1.20%	0.00%	0.00%	NA
Tropical Japonica	504	86.30%	13.70%	0.00%	0.00%	NA
Japonica Intermediate	241	83.00%	17.00%	0.00%	0.00%	NA
VI/Aromatic	96	36.50%	63.50%	0.00%	0.00%	NA
Intermediate	90	48.90%	51.10%	0.00%	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
vg0413703292	C -> T	LOC_Os04g23960.1	downstream_gene_variant ; 2834.0bp to feature; MODIFIER	silent_mutation	Average:34.835; most accessible tissue: Zhenshan97 young leaf, score: 47.986	N	N	N	N
vg0413703292	C -> T	LOC_Os04g23970.1	downstream_gene_variant ; 366.0bp to feature; MODIFIER	silent_mutation	Average:34.835; most accessible tissue: Zhenshan97 young leaf, score: 47.986	N	N	N	N
vg0413703292	C -> T	LOC_Os04g23980.1	downstream_gene_variant ; 3032.0bp to feature; MODIFIER	silent_mutation	Average:34.835; most accessible tissue: Zhenshan97 young leaf, score: 47.986	N	N	N	N
vg0413703292	C -> T	LOC_Os04g23970-LOC_Os04g23980	intergenic_region ; MODIFIER	silent_mutation	Average:34.835; most accessible tissue: Zhenshan97 young leaf, score: 47.986	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0413703292	8.01E-13	6.52E-15	mr1350_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
vg0413703292	NA	1.51E-06	mr1730_2	Jap_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
vg0413703292	NA	5.06E-15	mr1866_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