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Detailed information for vg0410688931:

Variant ID: vg0410688931 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 10688931
Reference Allele: A	Alternative Allele: T
Primary Allele: A	Secondary Allele: T

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 300. )

Flanking Sequence (100 bp) in Reference Genome:

TTGGCATCAAGGATTGTAACCTGTCAGCAAAAACCTTGCACAGGATTTTAACAGAGAAGTTCATCAATGAGATTGGTCTATAATCATTGGGGGTTTGAGG[A/T]
CTTGGTTTCTTTGGGACCAAGGTGATATACGAAAAATTGATAGAAGACAAATCCACCGAGTTTCCCCAAAATACAAGGGGACTTGGTCAAGCCCGAATGA

Reverse complement sequence

TCATTCGGGCTTGACCAAGTCCCCTTGTATTTTGGGGAAACTCGGTGGATTTGTCTTCTATCAATTTTTCGTATATCACCTTGGTCCCAAAGAAACCAAG[T/A]
CCTCAAACCCCCAATGATTATAGACCAATCTCATTGATGAACTTCTCTGTTAAAATCCTGTGCAAGGTTTTTGCTGACAGGTTACAATCCTTGATGCCAA

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	83.30%	1.90%	1.80%	12.97%	NA
All Indica	2759	99.60%	0.00%	0.07%	0.29%	NA
All Japonica	1512	54.20%	6.00%	4.70%	35.05%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	98.90%	0.00%	0.22%	0.86%	NA
Indica III	913	99.80%	0.00%	0.00%	0.22%	NA
Indica Intermediate	786	99.60%	0.00%	0.13%	0.25%	NA
Temperate Japonica	767	80.10%	10.70%	6.13%	3.13%	NA
Tropical Japonica	504	7.50%	1.40%	3.57%	87.50%	NA
Japonica Intermediate	241	69.70%	0.80%	2.49%	26.97%	NA
VI/Aromatic	96	30.20%	0.00%	9.38%	60.42%	NA
Intermediate	90	77.80%	0.00%	3.33%	18.89%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0410688931	A -> DEL	N	N	silent_mutation	Average:38.945; most accessible tissue: Callus, score: 57.588	N	N	N	N
vg0410688931	A -> T	LOC_Os04g19250.1	upstream_gene_variant ; 295.0bp to feature; MODIFIER	silent_mutation	Average:38.945; most accessible tissue: Callus, score: 57.588	N	N	N	N
vg0410688931	A -> T	LOC_Os04g19240.1	downstream_gene_variant ; 2529.0bp to feature; MODIFIER	silent_mutation	Average:38.945; most accessible tissue: Callus, score: 57.588	N	N	N	N
vg0410688931	A -> T	LOC_Os04g19240-LOC_Os04g19250	intergenic_region ; MODIFIER	silent_mutation	Average:38.945; most accessible tissue: Callus, score: 57.588	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0410688931	6.97E-07	9.39E-08	mr1035	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
vg0410688931	2.67E-07	7.81E-13	mr1062	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
vg0410688931	4.00E-07	4.00E-07	mr1525	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
vg0410688931	2.57E-06	4.96E-07	mr1626	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
vg0410688931	4.00E-09	9.95E-13	mr1062_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
vg0410688931	5.20E-06	5.20E-06	mr1525_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
vg0410688931	4.31E-07	1.36E-10	mr1631_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