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Detailed information for vg0715152264:

Variant ID: vg0715152264 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 15152264
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CTGGGCATCAGTCAAACTTAAGCTGTAGCACTTATTCCTCATCTCTCCGAATCTCTGAATATATTCATGCACAGGCTCATCATGTCTTTGCTTGATTGAT[G/A]
TCAGATCGGACAATTTCATCTCATGAACCCCACTTTAAAAATAGTTGTGAAACTATTTTTTTAAATCGGCCCAACTGTTAATTGATCCATATGGTAAAGA

Reverse complement sequence

TCTTTACCATATGGATCAATTAACAGTTGGGCCGATTTAAAAAAATAGTTTCACAACTATTTTTAAAGTGGGGTTCATGAGATGAAATTGTCCGATCTGA[C/T]
ATCAATCAAGCAAAGACATGATGAGCCTGTGCATGAATATATTCAGAGATTCGGAGAGATGAGGAATAAGTGCTACAGCTTAAGTTTGACTGATGCCCAG

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	38.80%	5.70%	25.77%	29.71%	NA
All Indica	2759	18.00%	0.00%	35.77%	46.21%	NA
All Japonica	1512	77.00%	17.30%	3.70%	2.05%	NA
Aus	269	29.00%	0.00%	48.33%	22.68%	NA
Indica I	595	21.50%	0.20%	45.38%	32.94%	NA
Indica II	465	27.50%	0.00%	37.20%	35.27%	NA
Indica III	913	6.20%	0.00%	26.62%	67.14%	NA
Indica Intermediate	786	23.30%	0.00%	38.30%	38.42%	NA
Temperate Japonica	767	91.50%	0.40%	4.95%	3.13%	NA
Tropical Japonica	504	45.80%	50.40%	3.17%	0.60%	NA
Japonica Intermediate	241	95.90%	1.70%	0.83%	1.66%	NA
VI/Aromatic	96	51.00%	0.00%	27.08%	21.88%	NA
Intermediate	90	52.20%	8.90%	21.11%	17.78%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0715152264	G -> DEL	N	N	silent_mutation	Average:17.362; most accessible tissue: Minghui63 young leaf, score: 31.294	N	N	N	N
vg0715152264	G -> A	LOC_Os07g26350.1	downstream_gene_variant ; 4842.0bp to feature; MODIFIER	silent_mutation	Average:17.362; most accessible tissue: Minghui63 young leaf, score: 31.294	N	N	N	N
vg0715152264	G -> A	LOC_Os07g26370.1	downstream_gene_variant ; 3473.0bp to feature; MODIFIER	silent_mutation	Average:17.362; most accessible tissue: Minghui63 young leaf, score: 31.294	N	N	N	N
vg0715152264	G -> A	LOC_Os07g26360.1	intron_variant ; MODIFIER	silent_mutation	Average:17.362; most accessible tissue: Minghui63 young leaf, score: 31.294	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0715152264	NA	1.01E-07	mr1551	Jap_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
vg0715152264	NA	7.31E-08	mr1552	Jap_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
vg0715152264	2.40E-06	NA	mr1159_2	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
vg0715152264	NA	4.08E-08	mr1335_2	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
vg0715152264	NA	2.35E-08	mr1363_2	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
vg0715152264	NA	6.16E-07	mr1363_2	Jap_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
vg0715152264	NA	5.02E-06	mr1397_2	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
vg0715152264	NA	3.73E-06	mr1524_2	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
vg0715152264	NA	2.02E-10	mr1800_2	Jap_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
vg0715152264	NA	2.56E-10	mr1851_2	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
vg0715152264	NA	1.82E-08	mr1862_2	Jap_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
vg0715152264	NA	1.56E-15	mr1864_2	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