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Detailed information for vg0609448033:

Variant ID: vg0609448033 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 9448033
Reference Allele: A	Alternative Allele: G
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GGGGTACTAAGGCGCATGGTGACATGTTGTGGGATTGTGTCTTGTGGGTACAGTGGTACACCTCTGATCAGAGTAAAACTATTTGAATAGCCGTGCCCGC[A/G]
GTTATGGGTGAGTTGAGCAATGTTTTTCGTGATTAGTCTCGCACTATTCATTAATGGTAATTGTGCTAATTAATGTGATTCCTGGTTTAGAATGGCATAT

Reverse complement sequence

ATATGCCATTCTAAACCAGGAATCACATTAATTAGCACAATTACCATTAATGAATAGTGCGAGACTAATCACGAAAAACATTGCTCAACTCACCCATAAC[T/C]
GCGGGCACGGCTATTCAAATAGTTTTACTCTGATCAGAGGTGTACCACTGTACCCACAAGACACAATCCCACAACATGTCACCATGCGCCTTAGTACCCC

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	57.60%	2.00%	4.06%	36.35%	NA
All Indica	2759	83.90%	0.10%	1.88%	14.06%	NA
All Japonica	1512	22.30%	5.90%	4.83%	67.00%	NA
Aus	269	5.20%	0.70%	16.73%	77.32%	NA
Indica I	595	86.20%	0.20%	1.51%	12.10%	NA
Indica II	465	84.10%	0.00%	1.51%	14.41%	NA
Indica III	913	82.90%	0.00%	1.42%	15.66%	NA
Indica Intermediate	786	83.30%	0.30%	2.93%	13.49%	NA
Temperate Japonica	767	39.40%	10.20%	8.34%	42.11%	NA
Tropical Japonica	504	2.40%	1.40%	1.19%	95.04%	NA
Japonica Intermediate	241	9.50%	1.70%	1.24%	87.55%	NA
VI/Aromatic	96	11.50%	1.00%	14.58%	72.92%	NA
Intermediate	90	47.80%	0.00%	8.89%	43.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0609448033	A -> G	LOC_Os06g16460-LOC_Os06g16470	intergenic_region ; MODIFIER	silent_mutation	Average:52.346; most accessible tissue: Minghui63 flag leaf, score: 70.17	N	N	N	N
vg0609448033	A -> DEL	N	N	silent_mutation	Average:52.346; most accessible tissue: Minghui63 flag leaf, score: 70.17	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0609448033	3.13E-06	NA	mr1968	Jap_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