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Detailed information for vg0104617666:

Variant ID: vg0104617666 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 4617666
Reference Allele: C	Alternative Allele: A
Primary Allele: C	Secondary Allele: A

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.96, A: 0.04, others allele: 0.00, population size: 104. )

Flanking Sequence (100 bp) in Reference Genome:

CAAAAAACACACCGTTTAGCGGTTTGAAAAATGTGCGCGCGGAAAACGAGGGTAGGGAGTTGGGAACCCTGGGTTCCAAACATGTAGGACCGTAAAGGGC[C/A]
TTTCCCACCCCAAAAGCTAGCCATTGAGGTGAGGGACTCCCCCACTTATATCTTAGGTCCTTTGCCCTTTCACAACCAATGTGGTACTATTCAACAATCT

Reverse complement sequence

AGATTGTTGAATAGTACCACATTGGTTGTGAAAGGGCAAAGGACCTAAGATATAAGTGGGGGAGTCCCTCACCTCAATGGCTAGCTTTTGGGGTGGGAAA[G/T]
GCCCTTTACGGTCCTACATGTTTGGAACCCAGGGTTCCCAACTCCCTACCCTCGTTTTCCGCGCGCACATTTTTCAAACCGCTAAACGGTGTGTTTTTTG

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	61.40%	22.00%	0.66%	15.93%	NA
All Indica	2759	82.40%	1.10%	0.47%	16.02%	NA
All Japonica	1512	35.30%	62.10%	0.86%	1.79%	NA
Aus	269	11.90%	0.70%	1.12%	86.25%	NA
Indica I	595	70.30%	0.20%	1.01%	28.57%	NA
Indica II	465	94.80%	2.60%	0.00%	2.58%	NA
Indica III	913	81.40%	0.80%	0.33%	17.52%	NA
Indica Intermediate	786	85.40%	1.40%	0.51%	12.72%	NA
Temperate Japonica	767	22.70%	76.30%	0.52%	0.52%	NA
Tropical Japonica	504	65.10%	29.00%	1.59%	4.37%	NA
Japonica Intermediate	241	12.90%	86.30%	0.41%	0.41%	NA
VI/Aromatic	96	8.30%	50.00%	1.04%	40.62%	NA
Intermediate	90	62.20%	22.20%	1.11%	14.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0104617666	C -> A	LOC_Os01g09190.1	downstream_gene_variant ; 1839.0bp to feature; MODIFIER	silent_mutation	Average:58.194; most accessible tissue: Zhenshan97 panicle, score: 76.605	N	N	N	N
vg0104617666	C -> A	LOC_Os01g09200.1	downstream_gene_variant ; 4011.0bp to feature; MODIFIER	silent_mutation	Average:58.194; most accessible tissue: Zhenshan97 panicle, score: 76.605	N	N	N	N
vg0104617666	C -> A	LOC_Os01g09190-LOC_Os01g09200	intergenic_region ; MODIFIER	silent_mutation	Average:58.194; most accessible tissue: Zhenshan97 panicle, score: 76.605	N	N	N	N
vg0104617666	C -> DEL	N	N	silent_mutation	Average:58.194; most accessible tissue: Zhenshan97 panicle, score: 76.605	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0104617666	NA	1.95E-07	mr1295_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
vg0104617666	NA	2.20E-08	mr1746_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
vg0104617666	NA	2.24E-06	mr1785_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
vg0104617666	NA	2.10E-07	mr1821_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
vg0104617666	NA	1.53E-13	mr1827_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
vg0104617666	NA	5.88E-16	mr1842_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
vg0104617666	NA	3.17E-06	mr1982_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