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Detailed information for vg0412754396:

Variant ID: vg0412754396 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 12754396
Reference Allele: C	Alternative Allele: G
Primary Allele: C	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ATGCTAAGGTTTCGGCTAGCACTCAGCAAACAAGAAAGGGGATAAACTAGATTGAAATTCCCCATTATCAAGCAAAAGGGAATAAACAAGATTGAAATTT[C/G]
CCGAAATCCCCAATAAGCCGGATCCAATTGGCCTAAAATCCCCAAATGAGGAAGCCTAATTTTTGGGGGAAGAACCCTAAGTCACAAATATCCGAATTAA

Reverse complement sequence

TTAATTCGGATATTTGTGACTTAGGGTTCTTCCCCCAAAAATTAGGCTTCCTCATTTGGGGATTTTAGGCCAATTGGATCCGGCTTATTGGGGATTTCGG[G/C]
AAATTTCAATCTTGTTTATTCCCTTTTGCTTGATAATGGGGAATTTCAATCTAGTTTATCCCCTTTCTTGTTTGCTGAGTGCTAGCCGAAACCTTAGCAT

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	35.10%	1.60%	3.11%	60.20%	NA
All Indica	2759	5.50%	0.00%	3.19%	91.34%	NA
All Japonica	1512	90.30%	4.80%	3.11%	1.72%	NA
Aus	269	3.00%	0.00%	1.49%	95.54%	NA
Indica I	595	5.20%	0.00%	2.52%	92.27%	NA
Indica II	465	9.20%	0.00%	1.29%	89.46%	NA
Indica III	913	3.00%	0.00%	5.70%	91.35%	NA
Indica Intermediate	786	6.40%	0.00%	1.91%	91.73%	NA
Temperate Japonica	767	84.00%	8.90%	5.61%	1.56%	NA
Tropical Japonica	504	98.60%	0.20%	0.00%	1.19%	NA
Japonica Intermediate	241	93.40%	1.70%	1.66%	3.32%	NA
VI/Aromatic	96	90.60%	0.00%	0.00%	9.38%	NA
Intermediate	90	53.30%	1.10%	8.89%	36.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0412754396	C -> DEL	N	N	silent_mutation	Average:9.4; most accessible tissue: Callus, score: 23.619	N	N	N	N
vg0412754396	C -> G	LOC_Os04g22510.1	upstream_gene_variant ; 3730.0bp to feature; MODIFIER	silent_mutation	Average:9.4; most accessible tissue: Callus, score: 23.619	N	N	N	N
vg0412754396	C -> G	LOC_Os04g22510-LOC_Os04g22520	intergenic_region ; MODIFIER	silent_mutation	Average:9.4; most accessible tissue: Callus, score: 23.619	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0412754396	8.77E-07	1.13E-08	mr1062_2	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