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Detailed information for vg0410969707:

Variant ID: vg0410969707 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 10969707
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TGGGAATTCATTATCACCCAGGAAAGGCTAATGTTGTAGCAGACGCTCTTAGCAGGAAAGGCTATTGCAATACTACGGAAGGACGACAGTTGCCATTGGA[G/A]
TTATGCAAGGAATTTGAAAGGTTGAATTTAGGAATTGTCAGTAGAGGTTTCGTCGCAGCCTTAGAAGCAAAGCCCACTCTAATTGATCAAGTTAGAGAGG

Reverse complement sequence

CCTCTCTAACTTGATCAATTAGAGTGGGCTTTGCTTCTAAGGCTGCGACGAAACCTCTACTGACAATTCCTAAATTCAACCTTTCAAATTCCTTGCATAA[C/T]
TCCAATGGCAACTGTCGTCCTTCCGTAGTATTGCAATAGCCTTTCCTGCTAAGAGCGTCTGCTACAACATTAGCCTTTCCTGGGTGATAATGAATTCCCA

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	21.40%	0.30%	41.98%	36.33%	NA
All Indica	2759	2.20%	0.50%	60.06%	37.19%	NA
All Japonica	1512	61.10%	0.00%	0.93%	37.96%	NA
Aus	269	1.90%	0.00%	91.82%	6.32%	NA
Indica I	595	1.80%	0.00%	57.48%	40.67%	NA
Indica II	465	2.60%	0.00%	47.10%	50.32%	NA
Indica III	913	2.00%	1.30%	71.63%	25.08%	NA
Indica Intermediate	786	2.70%	0.30%	56.23%	40.84%	NA
Temperate Japonica	767	95.80%	0.00%	0.13%	4.04%	NA
Tropical Japonica	504	4.80%	0.00%	1.98%	93.25%	NA
Japonica Intermediate	241	68.50%	0.00%	1.24%	30.29%	NA
VI/Aromatic	96	0.00%	0.00%	40.62%	59.38%	NA
Intermediate	90	22.20%	0.00%	30.00%	47.78%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0410969707	G -> DEL	LOC_Os04g19660.1	N	frameshift_variant	Average:11.026; most accessible tissue: Callus, score: 18.996	N	N	N	N
vg0410969707	G -> A	LOC_Os04g19660.1	synonymous_variant ; p.Glu961Glu; LOW	synonymous_codon	Average:11.026; most accessible tissue: Callus, score: 18.996	N	N	N	N
vg0410969707	G -> A	LOC_Os04g19660.1	synonymous_variant ; p.Glu961Glu; LOW	nonsynonymous_codon ; E961V	Average:11.026; most accessible tissue: Callus, score: 18.996	possibly damaging	1.677	DELETERIOUS	0.01

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0410969707	7.37E-07	NA	mr1380	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
vg0410969707	4.33E-06	7.93E-06	mr1561	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