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Detailed information for vg0417367372:

Variant ID: vg0417367372 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 17367372
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ATATTGGACAATAGGGAAATTTAGGTCAAAGTCTGATGGAAAAGGCTTTGGTAGAAGACCCATTGTATAAGCTCTGTTGATAATGACCTGGAGAAGTTCA[G/A]
CTCCTAAAACAAAAGAGTATAGGTGACAGAGGATCACCTTGCCTTACTCCCCTCTTGCAATGAAAATTTTTTCCAGGTACCCCATTGATCAGAACTGAAG

Reverse complement sequence

CTTCAGTTCTGATCAATGGGGTACCTGGAAAAAATTTTCATTGCAAGAGGGGAGTAAGGCAAGGTGATCCTCTGTCACCTATACTCTTTTGTTTTAGGAG[C/T]
TGAACTTCTCCAGGTCATTATCAACAGAGCTTATACAATGGGTCTTCTACCAAAGCCTTTTCCATCAGACTTTGACCTAAATTTCCCTATTGTCCAATAT

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	86.60%	3.90%	1.02%	8.48%	NA
All Indica	2759	93.70%	2.40%	0.62%	3.33%	NA
All Japonica	1512	71.40%	6.70%	1.79%	20.17%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	77.00%	5.50%	2.52%	14.96%	NA
Indica II	465	99.80%	0.00%	0.00%	0.22%	NA
Indica III	913	98.70%	1.20%	0.11%	0.00%	NA
Indica Intermediate	786	96.90%	2.70%	0.13%	0.25%	NA
Temperate Japonica	767	64.70%	0.10%	1.17%	34.03%	NA
Tropical Japonica	504	90.50%	8.10%	0.79%	0.60%	NA
Japonica Intermediate	241	52.70%	24.50%	5.81%	17.01%	NA
VI/Aromatic	96	85.40%	13.50%	0.00%	1.04%	NA
Intermediate	90	85.60%	6.70%	4.44%	3.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0417367372	G -> DEL	LOC_Os04g29290.1	N	frameshift_variant	Average:44.42; most accessible tissue: Minghui63 young leaf, score: 66.656	N	N	N	N
vg0417367372	G -> A	LOC_Os04g29290.1	missense_variant ; p.Ala114Val; MODERATE	nonsynonymous_codon ; A114V	Average:44.42; most accessible tissue: Minghui63 young leaf, score: 66.656	benign	1.273	TOLERATED	0.10

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0417367372	4.40E-07	NA	mr1004	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
vg0417367372	NA	3.71E-07	mr1221	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