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Detailed information for vg0818718847:

Variant ID: vg0818718847 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 18718847
Reference Allele: T	Alternative Allele: A
Primary Allele: T	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TACGTATAGTATCCATCTAGAAGTCATAAATATGAAACAAACTCGGATATCCAAAGAAACAACCCGAAACCGAAACCGAAACCGACACAGCGTCGGCCGG[T/A]
CTGACTGCACGGATACCGCCGGTCTGACCGGACCACATATCCAGCAACACTTGTAAATCCAAACATCTCCAAAACCACTTCGAAGATTAATTCCAAATAT

Reverse complement sequence

ATATTTGGAATTAATCTTCGAAGTGGTTTTGGAGATGTTTGGATTTACAAGTGTTGCTGGATATGTGGTCCGGTCAGACCGGCGGTATCCGTGCAGTCAG[A/T]
CCGGCCGACGCTGTGTCGGTTTCGGTTTCGGTTTCGGGTTGTTTCTTTGGATATCCGAGTTTGTTTCATATTTATGACTTCTAGATGGATACTATACGTA

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	82.60%	3.20%	0.85%	13.39%	NA
All Indica	2759	80.00%	1.60%	1.20%	17.18%	NA
All Japonica	1512	89.40%	0.00%	0.33%	10.32%	NA
Aus	269	61.70%	38.30%	0.00%	0.00%	NA
Indica I	595	96.30%	0.00%	0.17%	3.53%	NA
Indica II	465	89.00%	5.20%	0.65%	5.16%	NA
Indica III	913	70.20%	0.20%	1.31%	28.26%	NA
Indica Intermediate	786	73.80%	2.30%	2.16%	21.76%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	70.60%	0.00%	0.60%	28.77%	NA
Japonica Intermediate	241	94.60%	0.00%	0.83%	4.56%	NA
VI/Aromatic	96	96.90%	2.10%	1.04%	0.00%	NA
Intermediate	90	93.30%	2.20%	1.11%	3.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0818718847	T -> A	LOC_Os08g30420.1	upstream_gene_variant ; 1680.0bp to feature; MODIFIER	silent_mutation	Average:39.739; most accessible tissue: Minghui63 flag leaf, score: 51.386	N	N	N	N
vg0818718847	T -> A	LOC_Os08g30420-LOC_Os08g30430	intergenic_region ; MODIFIER	silent_mutation	Average:39.739; most accessible tissue: Minghui63 flag leaf, score: 51.386	N	N	N	N
vg0818718847	T -> DEL	N	N	silent_mutation	Average:39.739; most accessible tissue: Minghui63 flag leaf, score: 51.386	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0818718847	NA	6.16E-06	mr1438	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
vg0818718847	1.68E-07	1.19E-11	mr1836	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