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Detailed information for vg0623014227:

Variant ID: vg0623014227 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 23014227
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.92, A: 0.10, others allele: 0.00, population size: 59. )

Flanking Sequence (100 bp) in Reference Genome:

AAAAATACTTCCTCCATCTATTTTTGATAGTCATATTTCATCTTGATACACAGACTAAGGATAAGTAATTCTACTTATCATCTATTTAAACATGCTACTA[G/A]
TCATTACTCATAAACAAGTGATTCATTAATATTTACATTTCTCGATGCGCATAGAGCCAATCTTGTGTGGAAGAATGGAGAGTCACGCATTAAATCCGAG

Reverse complement sequence

CTCGGATTTAATGCGTGACTCTCCATTCTTCCACACAAGATTGGCTCTATGCGCATCGAGAAATGTAAATATTAATGAATCACTTGTTTATGAGTAATGA[C/T]
TAGTAGCATGTTTAAATAGATGATAAGTAGAATTACTTATCCTTAGTCTGTGTATCAAGATGAAATATGACTATCAAAAATAGATGGAGGAAGTATTTTT

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	43.70%	21.80%	0.78%	33.71%	NA
All Indica	2759	29.10%	35.80%	1.01%	34.07%	NA
All Japonica	1512	65.40%	1.30%	0.20%	33.07%	NA
Aus	269	62.10%	0.00%	1.86%	36.06%	NA
Indica I	595	4.20%	16.10%	2.02%	77.65%	NA
Indica II	465	27.30%	67.30%	0.65%	4.73%	NA
Indica III	913	45.50%	27.70%	0.77%	26.07%	NA
Indica Intermediate	786	30.20%	41.30%	0.76%	27.74%	NA
Temperate Japonica	767	52.30%	2.10%	0.26%	45.37%	NA
Tropical Japonica	504	83.70%	0.40%	0.00%	15.87%	NA
Japonica Intermediate	241	68.90%	0.80%	0.41%	29.88%	NA
VI/Aromatic	96	57.30%	1.00%	1.04%	40.62%	NA
Intermediate	90	54.40%	26.70%	0.00%	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
vg0623014227	G -> A	LOC_Os06g38780.1	upstream_gene_variant ; 3634.0bp to feature; MODIFIER	silent_mutation	Average:35.375; most accessible tissue: Minghui63 root, score: 76.425	N	N	N	N
vg0623014227	G -> A	LOC_Os06g38760.1	downstream_gene_variant ; 2756.0bp to feature; MODIFIER	silent_mutation	Average:35.375; most accessible tissue: Minghui63 root, score: 76.425	N	N	N	N
vg0623014227	G -> A	LOC_Os06g38770.1	downstream_gene_variant ; 2009.0bp to feature; MODIFIER	silent_mutation	Average:35.375; most accessible tissue: Minghui63 root, score: 76.425	N	N	N	N
vg0623014227	G -> A	LOC_Os06g38764.1	intron_variant ; MODIFIER	silent_mutation	Average:35.375; most accessible tissue: Minghui63 root, score: 76.425	N	N	N	N
vg0623014227	G -> DEL	N	N	silent_mutation	Average:35.375; most accessible tissue: Minghui63 root, score: 76.425	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0623014227	3.53E-07	3.53E-07	mr1427_2	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