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Detailed information for vg0402204023:

Variant ID: vg0402204023 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 2204023
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TGACTCTCTCTCAGCTGCTCCTTAAGTGTATCCATCATCCCGTGGCGATCGTTGTACTGGTCAGATAACTGCTGGAACTGGTCGCCGTGGACCTGGAGCT[G/A]
TGCCTTCAGTGAGTCTATCTCACTACCCCAAGCCTGGTGCTCCTCCTCTAGCTGAAGCTGCTACGCTGTGAGGTCAGTCACCTCGGTCTCTAACTCTCCC

Reverse complement sequence

GGGAGAGTTAGAGACCGAGGTGACTGACCTCACAGCGTAGCAGCTTCAGCTAGAGGAGGAGCACCAGGCTTGGGGTAGTGAGATAGACTCACTGAAGGCA[C/T]
AGCTCCAGGTCCACGGCGACCAGTTCCAGCAGTTATCTGACCAGTACAACGATCGCCACGGGATGATGGATACACTTAAGGAGCAGCTGAGAGAGAGTCA

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	45.70%	0.20%	5.12%	48.96%	NA
All Indica	2759	43.40%	0.30%	5.55%	50.78%	NA
All Japonica	1512	52.70%	0.00%	1.72%	45.57%	NA
Aus	269	35.70%	0.00%	21.19%	43.12%	NA
Indica I	595	27.70%	0.70%	3.53%	68.07%	NA
Indica II	465	50.30%	0.00%	1.72%	47.96%	NA
Indica III	913	48.70%	0.00%	9.53%	41.73%	NA
Indica Intermediate	786	45.00%	0.40%	4.71%	49.87%	NA
Temperate Japonica	767	74.40%	0.00%	0.39%	25.16%	NA
Tropical Japonica	504	23.40%	0.00%	4.37%	72.22%	NA
Japonica Intermediate	241	44.80%	0.00%	0.41%	54.77%	NA
VI/Aromatic	96	33.30%	0.00%	0.00%	66.67%	NA
Intermediate	90	43.30%	1.10%	6.67%	48.89%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0402204023	G -> DEL	N	N	silent_mutation	Average:15.736; most accessible tissue: Minghui63 panicle, score: 34.226	N	N	N	N
vg0402204023	G -> A	LOC_Os04g04600.1	upstream_gene_variant ; 2029.0bp to feature; MODIFIER	silent_mutation	Average:15.736; most accessible tissue: Minghui63 panicle, score: 34.226	N	N	N	N
vg0402204023	G -> A	LOC_Os04g04610.1	downstream_gene_variant ; 286.0bp to feature; MODIFIER	silent_mutation	Average:15.736; most accessible tissue: Minghui63 panicle, score: 34.226	N	N	N	N
vg0402204023	G -> A	LOC_Os04g04600-LOC_Os04g04610	intergenic_region ; MODIFIER	silent_mutation	Average:15.736; most accessible tissue: Minghui63 panicle, score: 34.226	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0402204023	4.37E-06	2.25E-07	mr1728	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