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Detailed information for vg0818009619:

Variant ID: vg0818009619 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 18009619
Reference Allele: T	Alternative Allele: G
Primary Allele: T	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CTCCCAAACCCTAGCCACCTCCCTCCACCAAATCCATCCGGTTCAACCGTCAAAATCACTCCGGTTACACCGTAAGTGAATCTCCTCCTCTTCCTCTCTC[T/G]
ATTCCATGGATTGATTTGAGTTTTTATTGAGTTTGTGATCCATGGCATGGAACCCTAGGTGAAGGAAGATGTGTTCTTCGATTTGCACCAATAGAGGGTA

Reverse complement sequence

TACCCTCTATTGGTGCAAATCGAAGAACACATCTTCCTTCACCTAGGGTTCCATGCCATGGATCACAAACTCAATAAAAACTCAAATCAATCCATGGAAT[A/C]
GAGAGAGGAAGAGGAGGAGATTCACTTACGGTGTAACCGGAGTGATTTTGACGGTTGAACCGGATGGATTTGGTGGAGGGAGGTGGCTAGGGTTTGGGAG

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	85.30%	0.00%	6.14%	8.51%	NA
All Indica	2759	75.60%	0.00%	10.29%	14.06%	NA
All Japonica	1512	99.70%	0.00%	0.13%	0.13%	NA
Aus	269	95.50%	0.00%	0.74%	3.72%	NA
Indica I	595	81.80%	0.20%	11.60%	6.39%	NA
Indica II	465	78.50%	0.00%	10.32%	11.18%	NA
Indica III	913	68.20%	0.00%	10.08%	21.69%	NA
Indica Intermediate	786	77.70%	0.00%	9.54%	12.72%	NA
Temperate Japonica	767	99.90%	0.00%	0.13%	0.00%	NA
Tropical Japonica	504	99.40%	0.00%	0.20%	0.40%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	99.00%	0.00%	1.04%	0.00%	NA
Intermediate	90	96.70%	0.00%	1.11%	2.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0818009619	T -> G	LOC_Os08g29360.1	intron_variant ; MODIFIER	silent_mutation	Average:48.3; most accessible tissue: Zhenshan97 flag leaf, score: 70.007	N	N	N	N
vg0818009619	T -> DEL	N	N	silent_mutation	Average:48.3; most accessible tissue: Zhenshan97 flag leaf, score: 70.007	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0818009619	1.78E-06	1.78E-06	mr1416_2	Ind_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