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Detailed information for vg0112624374:

Variant ID: vg0112624374 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 12624374
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GAATCGGGTGGGTCTACTGTATATATATATATGCATTTAGATTGAACCATGTAACCAATTCATTTCCATATAAGACAGCCTAGTGCTATGCTAAAGTAGT[G/A]
CAAATCAATGAATAAAGGGAATATATCCATACATACACAAAAAAGATTAAGTGCTGACCTTGTTGTGTTGCTTAACTAAACGCAATGAGTTTGAATCCTT

Reverse complement sequence

AAGGATTCAAACTCATTGCGTTTAGTTAAGCAACACAACAAGGTCAGCACTTAATCTTTTTTGTGTATGTATGGATATATTCCCTTTATTCATTGATTTG[C/T]
ACTACTTTAGCATAGCACTAGGCTGTCTTATATGGAAATGAATTGGTTACATGGTTCAATCTAAATGCATATATATATATACAGTAGACCCACCCGATTC

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	36.00%	0.30%	7.00%	56.62%	NA
All Indica	2759	9.20%	0.60%	10.00%	80.25%	NA
All Japonica	1512	84.20%	0.00%	0.66%	15.15%	NA
Aus	269	24.90%	0.00%	13.01%	62.08%	NA
Indica I	595	5.50%	0.30%	9.75%	84.37%	NA
Indica II	465	11.00%	1.10%	14.41%	73.55%	NA
Indica III	913	11.30%	0.40%	7.78%	80.50%	NA
Indica Intermediate	786	8.40%	0.60%	10.18%	80.79%	NA
Temperate Japonica	767	93.50%	0.00%	0.39%	6.13%	NA
Tropical Japonica	504	71.80%	0.00%	0.99%	27.18%	NA
Japonica Intermediate	241	80.50%	0.00%	0.83%	18.67%	NA
VI/Aromatic	96	65.60%	0.00%	2.08%	32.29%	NA
Intermediate	90	52.20%	0.00%	8.89%	38.89%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0112624374	G -> A	LOC_Os01g22450.1	upstream_gene_variant ; 3652.0bp to feature; MODIFIER	silent_mutation	Average:6.627; most accessible tissue: Callus, score: 23.36	N	N	N	N
vg0112624374	G -> A	LOC_Os01g22440.1	downstream_gene_variant ; 2670.0bp to feature; MODIFIER	silent_mutation	Average:6.627; most accessible tissue: Callus, score: 23.36	N	N	N	N
vg0112624374	G -> A	LOC_Os01g22440-LOC_Os01g22450	intergenic_region ; MODIFIER	silent_mutation	Average:6.627; most accessible tissue: Callus, score: 23.36	N	N	N	N
vg0112624374	G -> DEL	N	N	silent_mutation	Average:6.627; most accessible tissue: Callus, score: 23.36	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0112624374	3.69E-06	3.69E-06	mr1831	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