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Detailed information for vg0106723726:

Variant ID: vg0106723726 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 6723726
Reference Allele: C	Alternative Allele: G
Primary Allele: C	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ACACGACACCTTTGACTTTGTGAGGAAAATATCGTCGTTGCCTAGCTTGCTGCCTCCAACGACACAACAGCTCCGACTTCATAAGAAGCGTCGTCATTTC[C/G]
AAGCCCGTTGCAAGGGATAAAGCAGCTTCAATATCTCATGGTGGACATCAGCCAAAGACATCGAGAAAACCACTTCAAACACATGACAGGCACCAACACA

Reverse complement sequence

TGTGTTGGTGCCTGTCATGTGTTTGAAGTGGTTTTCTCGATGTCTTTGGCTGATGTCCACCATGAGATATTGAAGCTGCTTTATCCCTTGCAACGGGCTT[G/C]
GAAATGACGACGCTTCTTATGAAGTCGGAGCTGTTGTGTCGTTGGAGGCAGCAAGCTAGGCAACGACGATATTTTCCTCACAAAGTCAAAGGTGTCGTGT

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	93.90%	5.50%	0.61%	0.00%	NA
All Indica	2759	100.00%	0.00%	0.04%	0.00%	NA
All Japonica	1512	82.00%	16.20%	1.79%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	99.80%	0.00%	0.22%	0.00%	NA
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	100.00%	0.00%	0.00%	0.00%	NA
Temperate Japonica	767	84.40%	13.40%	2.22%	0.00%	NA
Tropical Japonica	504	77.40%	21.80%	0.79%	0.00%	NA
Japonica Intermediate	241	84.20%	13.30%	2.49%	0.00%	NA
VI/Aromatic	96	91.70%	8.30%	0.00%	0.00%	NA
Intermediate	90	92.20%	6.70%	1.11%	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
vg0106723726	C -> G	LOC_Os01g12304.1	upstream_gene_variant ; 3778.0bp to feature; MODIFIER	silent_mutation	Average:61.623; most accessible tissue: Zhenshan97 young leaf, score: 78.644	N	N	N	N
vg0106723726	C -> G	LOC_Os01g12310.1	downstream_gene_variant ; 1126.0bp to feature; MODIFIER	silent_mutation	Average:61.623; most accessible tissue: Zhenshan97 young leaf, score: 78.644	N	N	N	N
vg0106723726	C -> G	LOC_Os01g12320.1	downstream_gene_variant ; 1213.0bp to feature; MODIFIER	silent_mutation	Average:61.623; most accessible tissue: Zhenshan97 young leaf, score: 78.644	N	N	N	N
vg0106723726	C -> G	LOC_Os01g12320.3	downstream_gene_variant ; 1213.0bp to feature; MODIFIER	silent_mutation	Average:61.623; most accessible tissue: Zhenshan97 young leaf, score: 78.644	N	N	N	N
vg0106723726	C -> G	LOC_Os01g12320.2	downstream_gene_variant ; 1213.0bp to feature; MODIFIER	silent_mutation	Average:61.623; most accessible tissue: Zhenshan97 young leaf, score: 78.644	N	N	N	N
vg0106723726	C -> G	LOC_Os01g12310-LOC_Os01g12320	intergenic_region ; MODIFIER	silent_mutation	Average:61.623; most accessible tissue: Zhenshan97 young leaf, score: 78.644	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0106723726	2.29E-06	2.85E-06	mr1219	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