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Detailed information for vg0901410990:

Variant ID: vg0901410990 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 1410990
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.98, T: 0.02, others allele: 0.00, population size: 54. )

Flanking Sequence (100 bp) in Reference Genome:

CCTGAAGTCGATATCCGGCGGCGTGTCTTGGCGTATGTAGGCTTCCATGTTGTGGCTTCTATGTCGATTGTGTTGAGTGTTGATCCTCCATGGTGGGTGC[C/T]
GATCGTGTTGATCGTCTCCTCTCCCCTCTCCTCCTAAGGGGGCTTGTATTTATACTCATTGGTGTCCCCTTGTCCAAGTAGAACTAGGGAAACCAATATG

Reverse complement sequence

CATATTGGTTTCCCTAGTTCTACTTGGACAAGGGGACACCAATGAGTATAAATACAAGCCCCCTTAGGAGGAGAGGGGAGAGGAGACGATCAACACGATC[G/A]
GCACCCACCATGGAGGATCAACACTCAACACAATCGACATAGAAGCCACAACATGGAAGCCTACATACGCCAAGACACGCCGCCGGATATCGACTTCAGG

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	79.80%	7.70%	1.04%	11.51%	NA
All Indica	2759	93.70%	5.00%	0.18%	1.20%	NA
All Japonica	1512	69.00%	0.20%	0.33%	30.49%	NA
Aus	269	18.20%	81.40%	0.00%	0.37%	NA
Indica I	595	99.20%	0.30%	0.00%	0.50%	NA
Indica II	465	92.70%	7.10%	0.00%	0.22%	NA
Indica III	913	94.30%	4.10%	0.11%	1.53%	NA
Indica Intermediate	786	89.30%	8.30%	0.51%	1.91%	NA
Temperate Japonica	767	98.30%	0.00%	0.00%	1.69%	NA
Tropical Japonica	504	29.80%	0.40%	0.99%	68.85%	NA
Japonica Intermediate	241	57.70%	0.40%	0.00%	41.91%	NA
VI/Aromatic	96	24.00%	3.10%	38.54%	34.38%	NA
Intermediate	90	78.90%	1.10%	2.22%	17.78%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0901410990	C -> DEL	N	N	silent_mutation	Average:38.283; most accessible tissue: Zhenshan97 flag leaf, score: 77.203	N	N	N	N
vg0901410990	C -> T	LOC_Os09g02990.1	upstream_gene_variant ; 4163.0bp to feature; MODIFIER	silent_mutation	Average:38.283; most accessible tissue: Zhenshan97 flag leaf, score: 77.203	N	N	N	N
vg0901410990	C -> T	LOC_Os09g03000.1	upstream_gene_variant ; 496.0bp to feature; MODIFIER	silent_mutation	Average:38.283; most accessible tissue: Zhenshan97 flag leaf, score: 77.203	N	N	N	N
vg0901410990	C -> T	LOC_Os09g03010.1	downstream_gene_variant ; 4004.0bp to feature; MODIFIER	silent_mutation	Average:38.283; most accessible tissue: Zhenshan97 flag leaf, score: 77.203	N	N	N	N
vg0901410990	C -> T	LOC_Os09g03000-LOC_Os09g03010	intergenic_region ; MODIFIER	silent_mutation	Average:38.283; most accessible tissue: Zhenshan97 flag leaf, score: 77.203	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0901410990	NA	1.02E-06	mr1083	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
vg0901410990	1.61E-07	1.61E-07	mr1335_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