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Detailed information for vg0618384354:

Variant ID: vg0618384354 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 18384354
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GCATCACTTGAGAAGATGAGTTACCTGAGGGTGTTCCTAGCTGAGCGTGAGGTGATCCTTGTTCTTTATTTGGAGACCCAATCATCGAGTCGTTACCAGC[C/T]
TCAGGTCCTTGAGAAGTCGTCGTCTGCGCTTCAACTTCGGGAATTTCTTGATCTGGACCTACATCCGACTGGTTTCCAGTCGGGGGCTCTTGAGTTGTCG

Reverse complement sequence

CGACAACTCAAGAGCCCCCGACTGGAAACCAGTCGGATGTAGGTCCAGATCAAGAAATTCCCGAAGTTGAAGCGCAGACGACGACTTCTCAAGGACCTGA[G/A]
GCTGGTAACGACTCGATGATTGGGTCTCCAAATAAAGAACAAGGATCACCTCACGCTCAGCTAGGAACACCCTCAGGTAACTCATCTTCTCAAGTGATGC

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	81.30%	8.30%	10.01%	0.38%	NA
All Indica	2759	70.50%	13.50%	15.40%	0.58%	NA
All Japonica	1512	98.10%	0.10%	1.59%	0.13%	NA
Aus	269	91.80%	3.00%	5.20%	0.00%	NA
Indica I	595	70.60%	14.60%	13.95%	0.84%	NA
Indica II	465	66.20%	18.70%	14.84%	0.22%	NA
Indica III	913	70.90%	11.10%	17.52%	0.55%	NA
Indica Intermediate	786	72.60%	12.30%	14.38%	0.64%	NA
Temperate Japonica	767	96.70%	0.00%	3.00%	0.26%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	98.80%	0.80%	0.41%	0.00%	NA
VI/Aromatic	96	91.70%	5.20%	3.12%	0.00%	NA
Intermediate	90	86.70%	5.60%	7.78%	0.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0618384354	C -> T	LOC_Os06g31630.1	synonymous_variant ; p.Glu342Glu; LOW	synonymous_codon	Average:12.363; most accessible tissue: Callus, score: 18.286	N	N	N	N
vg0618384354	C -> DEL	LOC_Os06g31630.1	N	frameshift_variant	Average:12.363; most accessible tissue: Callus, score: 18.286	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0618384354	9.23E-07	NA	mr1586	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
vg0618384354	NA	2.43E-06	mr1881	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