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Detailed information for vg0618987742:

Variant ID: vg0618987742 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 18987742
Reference Allele: A	Alternative Allele: T
Primary Allele: A	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GTCAAACATTTTGAAATGGAGGGAGTACTACTTTATGAATGAGTACTCGAAGAATTGATACGTTATATGATCAGATCAGCCACAACATAAGTGAACAAAT[A/T]
CAGCAAACATTTGTAATATTTCATTATCTAAGATATTGAAGAAACTGTTTTGTATATATGCTGCAGAGTCGAAGGTTGTGACAAATTCTCCAAGTGGTCA

Reverse complement sequence

TGACCACTTGGAGAATTTGTCACAACCTTCGACTCTGCAGCATATATACAAAACAGTTTCTTCAATATCTTAGATAATGAAATATTACAAATGTTTGCTG[T/A]
ATTTGTTCACTTATGTTGTGGCTGATCTGATCATATAACGTATCAATTCTTCGAGTACTCATTCATAAAGTAGTACTCCCTCCATTTCAAAATGTTTGAC

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	91.20%	6.90%	0.00%	1.99%	NA
All Indica	2759	95.80%	4.00%	0.00%	0.22%	NA
All Japonica	1512	90.90%	3.70%	0.00%	5.36%	NA
Aus	269	44.60%	55.40%	0.00%	0.00%	NA
Indica I	595	99.00%	0.20%	0.00%	0.84%	NA
Indica II	465	100.00%	0.00%	0.00%	0.00%	NA
Indica III	913	94.00%	6.00%	0.00%	0.00%	NA
Indica Intermediate	786	92.90%	7.00%	0.00%	0.13%	NA
Temperate Japonica	767	93.50%	0.10%	0.00%	6.39%	NA
Tropical Japonica	504	87.10%	10.90%	0.00%	1.98%	NA
Japonica Intermediate	241	90.90%	0.00%	0.00%	9.13%	NA
VI/Aromatic	96	93.80%	2.10%	0.00%	4.17%	NA
Intermediate	90	90.00%	6.70%	0.00%	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
vg0618987742	A -> T	LOC_Os06g32650.1	downstream_gene_variant ; 1799.0bp to feature; MODIFIER	silent_mutation	Average:51.358; most accessible tissue: Minghui63 panicle, score: 62.157	N	N	N	N
vg0618987742	A -> T	LOC_Os06g32650-LOC_Os06g32660	intergenic_region ; MODIFIER	silent_mutation	Average:51.358; most accessible tissue: Minghui63 panicle, score: 62.157	N	N	N	N
vg0618987742	A -> DEL	N	N	silent_mutation	Average:51.358; most accessible tissue: Minghui63 panicle, score: 62.157	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0618987742	1.08E-09	NA	mr1033_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