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Detailed information for vg0418308850:

Variant ID: vg0418308850 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 18308850
Reference Allele: G	Alternative Allele: T
Primary Allele: G	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GCTAACACAATAGGAGGATGTCTAGAATTATGAGCATAAGGGTCAAAACCTAAACCACGGTTATGTGTGCTAACCTTAGATTGATCCAAAATCATGTTGA[G/T]
GTTCTTTTTACCATCAGAAAATCTTTGAAAAGAATTTTTCAAATAAGAAACCTCCTTTTCCAAATTAGCACAATTTTCACAATCTACCATGAAACCTTGG

Reverse complement sequence

CCAAGGTTTCATGGTAGATTGTGAAAATTGTGCTAATTTGGAAAAGGAGGTTTCTTATTTGAAAAATTCTTTTCAAAGATTTTCTGATGGTAAAAAGAAC[C/A]
TCAACATGATTTTGGATCAATCTAAGGTTAGCACACATAACCGTGGTTTAGGTTTTGACCCTTATGCTCATAATTCTAGACATCCTCCTATTGTGTTAGC

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	62.00%	2.10%	5.48%	30.41%	NA
All Indica	2759	55.30%	0.80%	1.88%	41.94%	NA
All Japonica	1512	67.00%	5.20%	13.03%	14.81%	NA
Aus	269	87.00%	0.00%	0.00%	13.01%	NA
Indica I	595	56.00%	0.70%	1.01%	42.35%	NA
Indica II	465	65.20%	0.40%	1.94%	32.47%	NA
Indica III	913	53.30%	1.10%	2.41%	43.15%	NA
Indica Intermediate	786	51.40%	0.90%	1.91%	45.80%	NA
Temperate Japonica	767	91.10%	1.30%	2.22%	5.35%	NA
Tropical Japonica	504	44.20%	9.90%	22.82%	23.02%	NA
Japonica Intermediate	241	37.80%	7.50%	26.97%	27.80%	NA
VI/Aromatic	96	90.60%	0.00%	4.17%	5.21%	NA
Intermediate	90	75.60%	0.00%	6.67%	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
vg0418308850	G -> DEL	N	N	silent_mutation	Average:12.742; most accessible tissue: Zhenshan97 root, score: 25.639	N	N	N	N
vg0418308850	G -> T	LOC_Os04g30650.1	5_prime_UTR_variant ; 843.0bp to feature; MODIFIER	silent_mutation	Average:12.742; most accessible tissue: Zhenshan97 root, score: 25.639	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0418308850	NA	9.79E-06	mr1798	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
vg0418308850	4.86E-07	3.15E-09	mr1800_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