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Detailed information for vg1022814760:

Variant ID: vg1022814760 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 22814760
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GGACCGGTTCGCGGGAAACCCGTACTTACCACAAGCTAGCGTGGGCAACGGCTGGGCTTGTAGTGTAGCTTTCCTCTAGCTGACGCATCCAGGCAAGGGT[G/A]
AGCGTGATGGAGTTCGGATGGGCCCTGCGACGGCCTATGCGACTTTTGGATTCACCTAGGCACGAGAGGGGACTGCCCACTGCCTTGCGATGAGTGGGGG

Reverse complement sequence

CCCCCACTCATCGCAAGGCAGTGGGCAGTCCCCTCTCGTGCCTAGGTGAATCCAAAAGTCGCATAGGCCGTCGCAGGGCCCATCCGAACTCCATCACGCT[C/T]
ACCCTTGCCTGGATGCGTCAGCTAGAGGAAAGCTACACTACAAGCCCAGCCGTTGCCCACGCTAGCTTGTGGTAAGTACGGGTTTCCCGCGAACCGGTCC

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	40.20%	16.00%	26.39%	17.44%	NA
All Indica	2759	9.60%	26.80%	36.28%	27.29%	NA
All Japonica	1512	96.10%	0.30%	3.11%	0.53%	NA
Aus	269	16.70%	0.00%	63.57%	19.70%	NA
Indica I	595	13.30%	27.90%	15.97%	42.86%	NA
Indica II	465	5.80%	41.30%	29.25%	23.66%	NA
Indica III	913	8.70%	18.50%	55.53%	17.31%	NA
Indica Intermediate	786	10.20%	27.10%	33.46%	29.26%	NA
Temperate Japonica	767	99.20%	0.50%	0.00%	0.26%	NA
Tropical Japonica	504	89.90%	0.00%	8.93%	1.19%	NA
Japonica Intermediate	241	99.20%	0.00%	0.83%	0.00%	NA
VI/Aromatic	96	87.50%	0.00%	10.42%	2.08%	NA
Intermediate	90	58.90%	12.20%	20.00%	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
vg1022814760	G -> A	LOC_Os10g42364.1	upstream_gene_variant ; 4374.0bp to feature; MODIFIER	silent_mutation	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N
vg1022814760	G -> A	LOC_Os10g42390.1	upstream_gene_variant ; 3318.0bp to feature; MODIFIER	silent_mutation	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N
vg1022814760	G -> A	LOC_Os10g42400.1	downstream_gene_variant ; 4458.0bp to feature; MODIFIER	silent_mutation	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N
vg1022814760	G -> A	LOC_Os10g42364-LOC_Os10g42390	intergenic_region ; MODIFIER	silent_mutation	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N
vg1022814760	G -> DEL	N	N	silent_mutation	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1022814760	2.30E-06	2.30E-06	mr1250_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