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Detailed information for vg1000477670:

Variant ID: vg1000477670 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 477670
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TATTGCTCTGGTAGTTCAAGCTGCACAACACGGCTAGGTGGAGTTAGCACCCTTCTGGTGTCTATCCATTCTCTGTATTGACATCTCCTTGGTGGTTCCT[G/A]
GGAGAAAAGAATAGATGTGAAGCGAGCAAAGTTAGTAAATGTTGTGAGAAAATAAGGATTCATGATAATCAAAATATTCTTACCATGAAATCGTTGTCGA

Reverse complement sequence

TCGACAACGATTTCATGGTAAGAATATTTTGATTATCATGAATCCTTATTTTCTCACAACATTTACTAACTTTGCTCGCTTCACATCTATTCTTTTCTCC[C/T]
AGGAACCACCAAGGAGATGTCAATACAGAGAATGGATAGACACCAGAAGGGTGCTAACTCCACCTAGCCGTGTTGTGCAGCTTGAACTACCAGAGCAATA

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	77.20%	15.30%	0.87%	6.62%	NA
All Indica	2759	70.40%	25.80%	0.47%	3.37%	NA
All Japonica	1512	99.30%	0.20%	0.00%	0.53%	NA
Aus	269	28.30%	0.70%	9.67%	61.34%	NA
Indica I	595	58.20%	41.80%	0.00%	0.00%	NA
Indica II	465	94.40%	4.50%	0.43%	0.65%	NA
Indica III	913	68.00%	26.10%	0.77%	5.15%	NA
Indica Intermediate	786	68.10%	26.00%	0.51%	5.47%	NA
Temperate Japonica	767	99.60%	0.30%	0.00%	0.13%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	96.70%	0.40%	0.00%	2.90%	NA
VI/Aromatic	96	57.30%	1.00%	1.04%	40.62%	NA
Intermediate	90	83.30%	6.70%	1.11%	8.89%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1000477670	G -> A	LOC_Os10g01740.1	splice_region_variant&intron_variant ; LOW	silent_mutation	Average:19.712; most accessible tissue: Minghui63 panicle, score: 25.313	N	N	N	N
vg1000477670	G -> A	LOC_Os10g01730.1	downstream_gene_variant ; 1616.0bp to feature; MODIFIER	silent_mutation	Average:19.712; most accessible tissue: Minghui63 panicle, score: 25.313	N	N	N	N
vg1000477670	G -> DEL	N	N	silent_mutation	Average:19.712; most accessible tissue: Minghui63 panicle, score: 25.313	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1000477670	NA	9.55E-06	mr1904	Ind_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
vg1000477670	NA	8.84E-06	mr1648_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
vg1000477670	NA	5.86E-07	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
vg1000477670	NA	4.81E-06	mr1669_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