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Detailed information for vg0618221570:

Variant ID: vg0618221570 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 18221570
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CCACTAACCCGGAGTCTTGGCTCACCGTCTACAGTCTCGCAATTCGCGCAGCAGGGGGAGACAGCAAAGCCATAGCAAACTACTTGCCTGTGGCTCTAGC[G/A]
GATTCTGCCCGGTCCTGGCTTCATGGGTTACCCCGTGGCACAATCGGATCATGGGCAGAACTTCGCGACCACTTCATCGCCAACTTCTAGGGCACCTTTG

Reverse complement sequence

CAAAGGTGCCCTAGAAGTTGGCGATGAAGTGGTCGCGAAGTTCTGCCCATGATCCGATTGTGCCACGGGGTAACCCATGAAGCCAGGACCGGGCAGAATC[C/T]
GCTAGAGCCACAGGCAAGTAGTTTGCTATGGCTTTGCTGTCTCCCCCTGCTGCGCGAATTGCGAGACTGTAGACGGTGAGCCAAGACTCCGGGTTAGTGG

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	50.00%	2.40%	5.35%	42.23%	NA
All Indica	2759	28.20%	0.20%	7.76%	63.83%	NA
All Japonica	1512	94.30%	0.20%	0.26%	5.22%	NA
Aus	269	39.80%	0.40%	13.01%	46.84%	NA
Indica I	595	35.10%	0.00%	5.88%	58.99%	NA
Indica II	465	39.40%	0.00%	8.39%	52.26%	NA
Indica III	913	13.60%	0.20%	8.54%	77.66%	NA
Indica Intermediate	786	33.30%	0.50%	7.89%	58.27%	NA
Temperate Japonica	767	97.40%	0.00%	0.26%	2.35%	NA
Tropical Japonica	504	88.30%	0.00%	0.40%	11.31%	NA
Japonica Intermediate	241	97.10%	1.20%	0.00%	1.66%	NA
VI/Aromatic	96	2.10%	95.80%	0.00%	2.08%	NA
Intermediate	90	56.70%	12.20%	0.00%	31.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0618221570	G -> A	LOC_Os06g31310.1	synonymous_variant ; p.Ala414Ala; LOW	synonymous_codon	Average:8.306; most accessible tissue: Callus, score: 24.524	N	N	N	N
vg0618221570	G -> DEL	LOC_Os06g31310.1	N	frameshift_variant	Average:8.306; most accessible tissue: Callus, score: 24.524	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0618221570	NA	2.68E-07	mr1438_2	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
vg0618221570	NA	1.35E-06	mr1994_2	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251