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Detailed information for vg0519673741:

Variant ID: vg0519673741 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 19673741
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AAGTGTGCCCTGGACCGTGCGCTGGAAAGTATTTCCGACGGTTATCAGTCCGAAAGGCATCTTAACGTAGCAAAATACCCCGAACGGCGTAATGAACGCT[G/A]
TCTTCTCCTCATCCTCTTTTGCCATGCTGATTTGGTGGTAGCCAGAGTAAGCGTCGAGGAAGCTTAATAGCTCGCAACCGGCTGTTGAATCCACCAACTG

Reverse complement sequence

CAGTTGGTGGATTCAACAGCCGGTTGCGAGCTATTAAGCTTCCTCGACGCTTACTCTGGCTACCACCAAATCAGCATGGCAAAAGAGGATGAGGAGAAGA[C/T]
AGCGTTCATTACGCCGTTCGGGGTATTTTGCTACGTTAAGATGCCTTTCGGACTGATAACCGTCGGAAATACTTTCCAGCGCACGGTCCAGGGCACACTT

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	41.60%	0.50%	18.45%	39.42%	NA
All Indica	2759	24.90%	0.80%	28.42%	45.85%	NA
All Japonica	1512	64.80%	0.00%	3.11%	32.08%	NA
Aus	269	89.20%	0.40%	5.95%	4.46%	NA
Indica I	595	9.70%	0.70%	26.22%	63.36%	NA
Indica II	465	36.30%	0.00%	21.72%	41.94%	NA
Indica III	913	28.30%	1.40%	36.25%	34.06%	NA
Indica Intermediate	786	25.80%	0.60%	24.94%	48.60%	NA
Temperate Japonica	767	95.00%	0.00%	0.39%	4.56%	NA
Tropical Japonica	504	11.90%	0.00%	8.53%	79.56%	NA
Japonica Intermediate	241	79.30%	0.00%	0.41%	20.33%	NA
VI/Aromatic	96	17.70%	0.00%	9.38%	72.92%	NA
Intermediate	90	47.80%	0.00%	17.78%	34.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0519673741	G -> DEL	LOC_Os05g33490.1	N	frameshift_variant	Average:8.003; most accessible tissue: Callus, score: 24.128	N	N	N	N
vg0519673741	G -> A	LOC_Os05g33490.1	missense_variant ; p.Thr1123Ile; MODERATE	nonsynonymous_codon ; T1123I	Average:8.003; most accessible tissue: Callus, score: 24.128	benign	0.792	DELETERIOUS	0.02

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0519673741	1.25E-06	NA	mr1599	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
vg0519673741	3.64E-06	NA	mr1599	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