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Detailed information for vg0616969932:

Variant ID: vg0616969932 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 16969932
Reference Allele: G	Alternative Allele: C
Primary Allele: C	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GTGGTTGAAGAGATATGAGCTCTTAAAGATTAAAAAACAAATAAAAGAAAAAGGGAGTTATTATTCAGTGGGGCCTACTTGTCAATGCCTTCTCCTTCCT[G/C]
TTCTTCCTCTCGTTCTTTTTTTTTTCTTCTGTTTGGCAGCTGAGAGGTAACAGAGAGGAGGGCAAGCAAGGCGCCGGCTCTCCGGTGGCCTGGAGGTGAG

Reverse complement sequence

CTCACCTCCAGGCCACCGGAGAGCCGGCGCCTTGCTTGCCCTCCTCTCTGTTACCTCTCAGCTGCCAAACAGAAGAAAAAAAAAAGAACGAGAGGAAGAA[C/G]
AGGAAGGAGAAGGCATTGACAAGTAGGCCCCACTGAATAATAACTCCCTTTTTCTTTTATTTGTTTTTTAATCTTTAAGAGCTCATATCTCTTCAACCAC

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	67.30%	30.10%	1.57%	0.99%	NA
All Indica	2759	93.20%	3.00%	2.39%	1.41%	NA
All Japonica	1512	12.70%	86.60%	0.26%	0.46%	NA
Aus	269	97.00%	1.90%	0.74%	0.37%	NA
Indica I	595	92.90%	6.10%	0.84%	0.17%	NA
Indica II	465	97.40%	1.10%	0.86%	0.65%	NA
Indica III	913	92.70%	0.20%	4.71%	2.41%	NA
Indica Intermediate	786	91.50%	5.10%	1.78%	1.65%	NA
Temperate Japonica	767	2.60%	96.50%	0.52%	0.39%	NA
Tropical Japonica	504	29.40%	70.00%	0.00%	0.60%	NA
Japonica Intermediate	241	10.00%	89.60%	0.00%	0.41%	NA
VI/Aromatic	96	99.00%	1.00%	0.00%	0.00%	NA
Intermediate	90	68.90%	28.90%	2.22%	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
vg0616969932	G -> C	LOC_Os06g29590-LOC_Os06g29600	intergenic_region ; MODIFIER	silent_mutation	Average:67.988; most accessible tissue: Callus, score: 87.927	N	N	N	N
vg0616969932	G -> DEL	N	N	silent_mutation	Average:67.988; most accessible tissue: Callus, score: 87.927	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0616969932	2.33E-06	NA	mr1132	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