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Detailed information for vg0417760655:

Variant ID: vg0417760655 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 17760655
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AGAAAGAATGCTAGTAAATTGATTGGGATGCCAAGGGTATTCTAGCATCAGACCCACGTACCACTGAAACTGAACTTCAAGTTCAGAAAATTATACATTT[G/A]
CAAAGACTTGCAAATAACCTGCTAGATGCATTTACTAATTATAAAGGTGTGACTAAATCTTTCATTCCTGCTCTGAATGCGCCAGAAAGAGTGGAGGTAC

Reverse complement sequence

GTACCTCCACTCTTTCTGGCGCATTCAGAGCAGGAATGAAAGATTTAGTCACACCTTTATAATTAGTAAATGCATCTAGCAGGTTATTTGCAAGTCTTTG[C/T]
AAATGTATAATTTTCTGAACTTGAAGTTCAGTTTCAGTGGTACGTGGGTCTGATGCTAGAATACCCTTGGCATCCCAATCAATTTACTAGCATTCTTTCT

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	33.90%	0.10%	22.30%	43.63%	NA
All Indica	2759	39.40%	0.10%	32.62%	27.84%	NA
All Japonica	1512	15.50%	0.10%	5.36%	78.97%	NA
Aus	269	68.40%	0.00%	17.47%	14.13%	NA
Indica I	595	68.40%	0.30%	22.69%	8.57%	NA
Indica II	465	19.80%	0.00%	45.81%	34.41%	NA
Indica III	913	27.50%	0.10%	37.79%	34.61%	NA
Indica Intermediate	786	42.90%	0.10%	26.34%	30.66%	NA
Temperate Japonica	767	11.50%	0.00%	7.43%	81.10%	NA
Tropical Japonica	504	23.80%	0.40%	3.57%	72.22%	NA
Japonica Intermediate	241	11.20%	0.00%	2.49%	86.31%	NA
VI/Aromatic	96	62.50%	0.00%	1.04%	36.46%	NA
Intermediate	90	42.20%	0.00%	27.78%	30.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0417760655	G -> DEL	LOC_Os04g29800.1	N	frameshift_variant	Average:16.147; most accessible tissue: Callus, score: 36.007	N	N	N	N
vg0417760655	G -> A	LOC_Os04g29800.1	synonymous_variant ; p.Leu278Leu; LOW	synonymous_codon	Average:16.147; most accessible tissue: Callus, score: 36.007	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0417760655	4.77E-06	8.83E-06	mr1543	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