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Detailed information for vg0609457229:

Variant ID: vg0609457229 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 9457229
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GACTTTGAACAATTATTCAACTTTGCATTATCTGATTTGAGCATTTGCTATTCCTTTGCTACATATTTAAGCCTACCCAGAGCTCCACAGATTTGATTAC[G/A]
GCCGTACCGCAAGTGTTTGCCAAGGCATCGATATATCCAACCTCCATTGGGGTGCTTGGTTGAGTCGGTGTATGTCACCATTCCACTTGCATTGGTAAGA

Reverse complement sequence

TCTTACCAATGCAAGTGGAATGGTGACATACACCGACTCAACCAAGCACCCCAATGGAGGTTGGATATATCGATGCCTTGGCAAACACTTGCGGTACGGC[C/T]
GTAATCAAATCTGTGGAGCTCTGGGTAGGCTTAAATATGTAGCAAAGGAATAGCAAATGCTCAAATCAGATAATGCAAAGTTGAATAATTGTTCAAAGTC

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	57.90%	0.20%	2.75%	39.19%	NA
All Indica	2759	78.70%	0.10%	3.08%	18.16%	NA
All Japonica	1512	32.80%	0.10%	0.60%	66.47%	NA
Aus	269	5.20%	0.40%	11.90%	82.53%	NA
Indica I	595	85.20%	0.00%	2.35%	12.44%	NA
Indica II	465	83.40%	0.20%	1.51%	14.84%	NA
Indica III	913	71.50%	0.00%	4.16%	24.32%	NA
Indica Intermediate	786	79.30%	0.10%	3.31%	17.30%	NA
Temperate Japonica	767	57.00%	0.00%	0.26%	42.76%	NA
Tropical Japonica	504	5.60%	0.40%	0.99%	93.06%	NA
Japonica Intermediate	241	12.90%	0.00%	0.83%	86.31%	NA
VI/Aromatic	96	8.30%	0.00%	1.04%	90.62%	NA
Intermediate	90	52.20%	3.30%	3.33%	41.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0609457229	G -> A	LOC_Os06g16470.1	upstream_gene_variant ; 214.0bp to feature; MODIFIER	silent_mutation	Average:39.103; most accessible tissue: Minghui63 flag leaf, score: 59.244	N	N	N	N
vg0609457229	G -> A	LOC_Os06g16480.1	downstream_gene_variant ; 4626.0bp to feature; MODIFIER	silent_mutation	Average:39.103; most accessible tissue: Minghui63 flag leaf, score: 59.244	N	N	N	N
vg0609457229	G -> A	LOC_Os06g16460-LOC_Os06g16470	intergenic_region ; MODIFIER	silent_mutation	Average:39.103; most accessible tissue: Minghui63 flag leaf, score: 59.244	N	N	N	N
vg0609457229	G -> DEL	N	N	silent_mutation	Average:39.103; most accessible tissue: Minghui63 flag leaf, score: 59.244	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0609457229	2.14E-07	2.24E-10	mr1221_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