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Detailed information for vg0727484366:

Variant ID: vg0727484366 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 27484366
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TTGCATGGGTTGCTTTTCACAAGTGAGCTGAGGCTTTCATGTAAGAAAATAATAAACTGAGGCTTGCAGGCGGTGCGCGGGGAGGAGGTGACGATCACCG[G/A]
CGAAGTTGAAATGAAGGCCGATAACGACGCTGCCGCCGAGCACCGCATCCAGATGCCGGAGTCAGGACGACAGGCGGATATGGCGGCCGCCGCCGCGCCG

Reverse complement sequence

CGGCGCGGCGGCGGCCGCCATATCCGCCTGTCGTCCTGACTCCGGCATCTGGATGCGGTGCTCGGCGGCAGCGTCGTTATCGGCCTTCATTTCAACTTCG[C/T]
CGGTGATCGTCACCTCCTCCCCGCGCACCGCCTGCAAGCCTCAGTTTATTATTTTCTTACATGAAAGCCTCAGCTCACTTGTGAAAAGCAACCCATGCAA

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	60.80%	2.40%	2.96%	33.88%	NA
All Indica	2759	47.10%	0.10%	3.88%	48.89%	NA
All Japonica	1512	91.40%	6.60%	0.86%	1.12%	NA
Aus	269	47.20%	1.10%	4.09%	47.58%	NA
Indica I	595	66.40%	0.20%	3.70%	29.75%	NA
Indica II	465	22.60%	0.20%	7.74%	69.46%	NA
Indica III	913	45.70%	0.10%	0.99%	53.23%	NA
Indica Intermediate	786	48.60%	0.10%	5.09%	46.18%	NA
Temperate Japonica	767	98.60%	0.30%	0.26%	0.91%	NA
Tropical Japonica	504	82.30%	15.10%	1.39%	1.19%	NA
Japonica Intermediate	241	87.60%	9.10%	1.66%	1.66%	NA
VI/Aromatic	96	12.50%	0.00%	4.17%	83.33%	NA
Intermediate	90	57.80%	6.70%	5.56%	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
vg0727484366	G -> DEL	N	N	silent_mutation	Average:11.418; most accessible tissue: Callus, score: 32.18	N	N	N	N
vg0727484366	G -> A	LOC_Os07g46039.1	upstream_gene_variant ; 4524.0bp to feature; MODIFIER	silent_mutation	Average:11.418; most accessible tissue: Callus, score: 32.18	N	N	N	N
vg0727484366	G -> A	LOC_Os07g46060.1	upstream_gene_variant ; 2205.0bp to feature; MODIFIER	silent_mutation	Average:11.418; most accessible tissue: Callus, score: 32.18	N	N	N	N
vg0727484366	G -> A	LOC_Os07g46039.2	upstream_gene_variant ; 4510.0bp to feature; MODIFIER	silent_mutation	Average:11.418; most accessible tissue: Callus, score: 32.18	N	N	N	N
vg0727484366	G -> A	LOC_Os07g46039-LOC_Os07g46060	intergenic_region ; MODIFIER	silent_mutation	Average:11.418; most accessible tissue: Callus, score: 32.18	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0727484366	1.23E-07	8.51E-09	mr1517_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
vg0727484366	2.15E-08	2.74E-09	mr1538_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