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Detailed information for vg1011502581:

Variant ID: vg1011502581 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 11502581
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CCAATGGTTCGGCCGAACCATGGGCTGGGCCAACCTGGCCCAATTTCAGTAGGCAGCCTCCTCTTTTGCTCTCATACGCAAACTTGTGAATTTTGGCCCA[G/A]
TTCATCGTGTCAATTCTGAGTTCTTGGCCCATTCATACATAAGTCTGATTCTCGACATCGTCCGATTGATTTATCGTCTGTGTTGATGTCGATTCTCCTC

Reverse complement sequence

GAGGAGAATCGACATCAACACAGACGATAAATCAATCGGACGATGTCGAGAATCAGACTTATGTATGAATGGGCCAAGAACTCAGAATTGACACGATGAA[C/T]
TGGGCCAAAATTCACAAGTTTGCGTATGAGAGCAAAAGAGGAGGCTGCCTACTGAAATTGGGCCAGGTTGGCCCAGCCCATGGTTCGGCCGAACCATTGG

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	22.70%	8.60%	9.88%	58.82%	NA
All Indica	2759	25.20%	2.80%	9.68%	62.31%	NA
All Japonica	1512	20.90%	21.00%	10.71%	47.42%	NA
Aus	269	6.70%	0.70%	9.29%	83.27%	NA
Indica I	595	23.50%	5.20%	22.86%	48.40%	NA
Indica II	465	18.10%	4.90%	11.40%	65.59%	NA
Indica III	913	30.20%	0.20%	0.44%	69.11%	NA
Indica Intermediate	786	24.80%	2.80%	9.41%	62.98%	NA
Temperate Japonica	767	36.20%	37.90%	10.17%	15.65%	NA
Tropical Japonica	504	4.60%	1.80%	8.33%	85.32%	NA
Japonica Intermediate	241	6.20%	7.10%	17.43%	69.29%	NA
VI/Aromatic	96	18.80%	0.00%	4.17%	77.08%	NA
Intermediate	90	28.90%	10.00%	10.00%	51.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1011502581	G -> A	LOC_Os10g22220.1	upstream_gene_variant ; 4502.0bp to feature; MODIFIER	silent_mutation	Average:12.068; most accessible tissue: Minghui63 flag leaf, score: 17.021	N	N	N	N
vg1011502581	G -> A	LOC_Os10g22230.1	downstream_gene_variant ; 3257.0bp to feature; MODIFIER	silent_mutation	Average:12.068; most accessible tissue: Minghui63 flag leaf, score: 17.021	N	N	N	N
vg1011502581	G -> A	LOC_Os10g22220-LOC_Os10g22230	intergenic_region ; MODIFIER	silent_mutation	Average:12.068; most accessible tissue: Minghui63 flag leaf, score: 17.021	N	N	N	N
vg1011502581	G -> DEL	N	N	silent_mutation	Average:12.068; most accessible tissue: Minghui63 flag leaf, score: 17.021	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1011502581	2.04E-06	2.04E-06	mr1609_2	Jap_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
vg1011502581	NA	3.29E-06	mr1959_2	Jap_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