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Detailed information for vg0518597457:

Variant ID: vg0518597457 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 18597457
Reference Allele: G	Alternative Allele: A,T
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TGTCTATTGTCCTATCCACAAGACAAAGAATCACGATCTCTCGAGCTGTAAAGTTCTCCTCGGCGCCATGAAAGCCCCGTCTCCTAAGTCATACGTCCCC[G/A,T]
CCAGGGATAACGGCAAGGAACAGGGAGCGACTCCAGCCTCAGATCGATTCGTTGGGGTAATCGATCTCGATCCTCACGAACCATCGGTCTTACATCTCCT

Reverse complement sequence

AGGAGATGTAAGACCGATGGTTCGTGAGGATCGAGATCGATTACCCCAACGAATCGATCTGAGGCTGGAGTCGCTCCCTGTTCCTTGCCGTTATCCCTGG[C/T,A]
GGGGACGTATGACTTAGGAGACGGGGCTTTCATGGCGCCGAGGAGAACTTTACAGCTCGAGAGATCGTGATTCTTTGTCTTGTGGATAGGACAATAGACA

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	47.00%	1.60%	7.17%	44.22%	T: 0.04%
All Indica	2759	17.10%	1.90%	8.99%	71.95%	T: 0.07%
All Japonica	1512	96.70%	0.10%	1.06%	2.18%	NA
Aus	269	53.90%	6.70%	23.42%	15.99%	NA
Indica I	595	3.90%	0.30%	3.19%	92.61%	NA
Indica II	465	11.40%	0.60%	7.31%	80.65%	NA
Indica III	913	29.70%	3.60%	14.79%	51.70%	T: 0.22%
Indica Intermediate	786	15.80%	1.90%	7.63%	74.68%	NA
Temperate Japonica	767	96.20%	0.10%	0.39%	3.26%	NA
Tropical Japonica	504	96.40%	0.00%	2.38%	1.19%	NA
Japonica Intermediate	241	98.80%	0.00%	0.41%	0.83%	NA
VI/Aromatic	96	96.90%	0.00%	2.08%	1.04%	NA
Intermediate	90	54.40%	3.30%	11.11%	31.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0518597457	G -> T	LOC_Os05g31930.1	missense_variant ; p.Ala122Ser; MODERATE	nonsynonymous_codon ; A122S	Average:7.579; most accessible tissue: Callus, score: 30.103	unknown	unknown	TOLERATED	0.07
vg0518597457	G -> DEL	LOC_Os05g31930.1	N	frameshift_variant	Average:7.579; most accessible tissue: Callus, score: 30.103	N	N	N	N
vg0518597457	G -> A	LOC_Os05g31930.1	missense_variant ; p.Ala122Thr; MODERATE	nonsynonymous_codon ; A122T	Average:7.579; most accessible tissue: Callus, score: 30.103	unknown	unknown	TOLERATED	0.17

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0518597457	4.98E-06	4.98E-06	mr1981_2	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