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Detailed information for vg0410973424:

Variant ID: vg0410973424 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 10973424
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GCACCAGACTGAGAAGTGGCGGAGATAAGCCCACGGGGGTTCGCTGGGGAGTCCATACCTTGTTTATAAGGGGGTGATTATGATCCGGGAGTGGTGCACT[G/A]
TGGTGGATTGTGTTGTACGAGAGGTAATGTCACAACTCTTTTCCGAGGTACCGTGGTGGTATTGAGGCACATGGTGACATGATGTGGGGTTGTGTCTTGT

Reverse complement sequence

ACAAGACACAACCCCACATCATGTCACCATGTGCCTCAATACCACCACGGTACCTCGGAAAAGAGTTGTGACATTACCTCTCGTACAACACAATCCACCA[C/T]
AGTGCACCACTCCCGGATCATAATCACCCCCTTATAAACAAGGTATGGACTCCCCAGCGAACCCCCGTGGGCTTATCTCCGCCACTTCTCAGTCTGGTGC

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	55.90%	4.40%	14.88%	24.84%	NA
All Indica	2759	47.80%	7.50%	22.83%	21.86%	NA
All Japonica	1512	63.70%	0.00%	3.31%	33.00%	NA
Aus	269	98.50%	0.00%	1.49%	0.00%	NA
Indica I	595	18.50%	17.60%	37.31%	26.55%	NA
Indica II	465	51.60%	2.20%	18.92%	27.31%	NA
Indica III	913	60.00%	4.90%	17.20%	17.85%	NA
Indica Intermediate	786	53.60%	6.00%	20.74%	19.72%	NA
Temperate Japonica	767	96.10%	0.00%	0.52%	3.39%	NA
Tropical Japonica	504	10.90%	0.00%	6.94%	82.14%	NA
Japonica Intermediate	241	71.00%	0.00%	4.56%	24.48%	NA
VI/Aromatic	96	38.50%	0.00%	3.12%	58.33%	NA
Intermediate	90	62.20%	2.20%	17.78%	17.78%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0410973424	G -> DEL	N	N	silent_mutation	Average:4.821; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N
vg0410973424	G -> A	LOC_Os04g19660.1	downstream_gene_variant ; 2178.0bp to feature; MODIFIER	silent_mutation	Average:4.821; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N
vg0410973424	G -> A	LOC_Os04g19670.1	downstream_gene_variant ; 1877.0bp to feature; MODIFIER	silent_mutation	Average:4.821; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N
vg0410973424	G -> A	LOC_Os04g19660-LOC_Os04g19670	intergenic_region ; MODIFIER	silent_mutation	Average:4.821; 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
vg0410973424	NA	3.18E-06	mr1029	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
vg0410973424	NA	6.98E-08	mr1734	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
vg0410973424	NA	8.11E-08	mr1925	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