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Detailed information for vg1000477626:

Variant ID: vg1000477626 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 477626
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 92. )

Flanking Sequence (100 bp) in Reference Genome:

GTGAGGATCCCTCTCCTCTCTCAAACCGCGTTTTAGTAACCCTGTATTGCTCTGGTAGTTCAAGCTGCACAACACGGCTAGGTGGAGTTAGCACCCTTCT[G/A]
GTGTCTATCCATTCTCTGTATTGACATCTCCTTGGTGGTTCCTGGGAGAAAAGAATAGATGTGAAGCGAGCAAAGTTAGTAAATGTTGTGAGAAAATAAG

Reverse complement sequence

CTTATTTTCTCACAACATTTACTAACTTTGCTCGCTTCACATCTATTCTTTTCTCCCAGGAACCACCAAGGAGATGTCAATACAGAGAATGGATAGACAC[C/T]
AGAAGGGTGCTAACTCCACCTAGCCGTGTTGTGCAGCTTGAACTACCAGAGCAATACAGGGTTACTAAAACGCGGTTTGAGAGAGGAGAGGGATCCTCAC

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	77.10%	15.20%	0.32%	7.32%	NA
All Indica	2759	70.20%	25.80%	0.29%	3.66%	NA
All Japonica	1512	99.30%	0.10%	0.07%	0.53%	NA
Aus	269	28.30%	0.70%	1.49%	69.52%	NA
Indica I	595	57.10%	42.90%	0.00%	0.00%	NA
Indica II	465	94.80%	4.30%	0.00%	0.86%	NA
Indica III	913	68.10%	25.60%	0.55%	5.70%	NA
Indica Intermediate	786	68.10%	25.80%	0.38%	5.73%	NA
Temperate Japonica	767	99.70%	0.10%	0.00%	0.13%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	96.70%	0.00%	0.41%	2.90%	NA
VI/Aromatic	96	56.20%	1.00%	0.00%	42.71%	NA
Intermediate	90	84.40%	3.30%	2.22%	10.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1000477626	G -> A	LOC_Os10g01740.1	synonymous_variant ; p.Thr15Thr; LOW	synonymous_codon	Average:19.913; most accessible tissue: Minghui63 panicle, score: 29.741	N	N	N	N
vg1000477626	G -> A	LOC_Os10g01740.1	synonymous_variant ; p.Thr15Thr; LOW	nonsynonymous_codon ; T15I	Average:19.913; most accessible tissue: Minghui63 panicle, score: 29.741	benign	0.472	DELETERIOUS	0.00
vg1000477626	G -> DEL	LOC_Os10g01740.1	N	frameshift_variant	Average:19.913; most accessible tissue: Minghui63 panicle, score: 29.741	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1000477626	NA	1.54E-06	mr1655_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