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Detailed information for vg0224620813:

Variant ID: vg0224620813 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 24620813
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AGTCTTGGCTTCCGCTTCCCTTTTGTAATGCAGTTGTGAGCTCGGGATCTGTCCGCAGCCTAACATGACTGTACCTCTACTCTATAATAAAGAGACCTCT[G/A]
TTGCTGTGATATTCTGTCTTCCTGTGATACCAGGACTGTTTCCTGGGACTGGTATCGATTAACAGGTTAATTTGGAGCGTCACGGGCTAGTTCCGGTCGG

Reverse complement sequence

CCGACCGGAACTAGCCCGTGACGCTCCAAATTAACCTGTTAATCGATACCAGTCCCAGGAAACAGTCCTGGTATCACAGGAAGACAGAATATCACAGCAA[C/T]
AGAGGTCTCTTTATTATAGAGTAGAGGTACAGTCATGTTAGGCTGCGGACAGATCCCGAGCTCACAACTGCATTACAAAAGGGAAGCGGAAGCCAAGACT

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	43.10%	8.50%	3.75%	44.65%	NA
All Indica	2759	31.50%	4.50%	4.35%	59.66%	NA
All Japonica	1512	62.30%	16.60%	1.46%	19.64%	NA
Aus	269	53.90%	3.70%	4.83%	37.55%	NA
Indica I	595	4.90%	0.70%	2.35%	92.10%	NA
Indica II	465	53.10%	1.10%	0.86%	44.95%	NA
Indica III	913	30.70%	7.80%	8.87%	52.68%	NA
Indica Intermediate	786	39.70%	5.70%	2.67%	51.91%	NA
Temperate Japonica	767	74.20%	11.90%	1.83%	12.13%	NA
Tropical Japonica	504	46.20%	19.80%	1.19%	32.74%	NA
Japonica Intermediate	241	58.10%	24.90%	0.83%	16.18%	NA
VI/Aromatic	96	35.40%	5.20%	16.67%	42.71%	NA
Intermediate	90	54.40%	11.10%	6.67%	27.78%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0224620813	G -> A	LOC_Os02g40580.1	upstream_gene_variant ; 2534.0bp to feature; MODIFIER	silent_mutation	Average:8.455; most accessible tissue: Callus, score: 23.074	N	N	N	N
vg0224620813	G -> A	LOC_Os02g40590.1	downstream_gene_variant ; 3934.0bp to feature; MODIFIER	silent_mutation	Average:8.455; most accessible tissue: Callus, score: 23.074	N	N	N	N
vg0224620813	G -> A	LOC_Os02g40580-LOC_Os02g40590	intergenic_region ; MODIFIER	silent_mutation	Average:8.455; most accessible tissue: Callus, score: 23.074	N	N	N	N
vg0224620813	G -> DEL	N	N	silent_mutation	Average:8.455; most accessible tissue: Callus, score: 23.074	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0224620813	5.05E-07	8.38E-09	mr1872	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