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Detailed information for vg1111310432:

Variant ID: vg1111310432 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 11310432
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GAATCCTATCATTAAGCCATGGCCATTCAGAGGTTGGGGAATTGATATGATCGGCATGATTAATCCACCATCGAGTAAAGGACATAAGTTTATATTGGTG[G/A]
CGACCGATTATTTCACCAAATGGGTAGAGGCGATTCCTTTGAAGAAGGTTGATTCTGGGGATGCGATACAGTTTGTTCAAGAGCATATAATCTACCGATT

Reverse complement sequence

AATCGGTAGATTATATGCTCTTGAACAAACTGTATCGCATCCCCAGAATCAACCTTCTTCAAAGGAATCGCCTCTACCCATTTGGTGAAATAATCGGTCG[C/T]
CACCAATATAAACTTATGTCCTTTACTCGATGGTGGATTAATCATGCCGATCATATCAATTCCCCAACCTCTGAATGGCCATGGCTTAATGATAGGATTC

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	63.30%	11.50%	25.07%	0.08%	NA
All Indica	2759	40.40%	19.20%	40.20%	0.14%	NA
All Japonica	1512	97.80%	0.50%	1.72%	0.00%	NA
Aus	269	88.50%	0.00%	11.52%	0.00%	NA
Indica I	595	23.70%	27.60%	48.57%	0.17%	NA
Indica II	465	65.60%	14.40%	19.57%	0.43%	NA
Indica III	913	33.40%	20.80%	45.78%	0.00%	NA
Indica Intermediate	786	46.30%	14.00%	39.57%	0.13%	NA
Temperate Japonica	767	97.70%	0.10%	2.22%	0.00%	NA
Tropical Japonica	504	97.40%	1.20%	1.39%	0.00%	NA
Japonica Intermediate	241	99.20%	0.00%	0.83%	0.00%	NA
VI/Aromatic	96	97.90%	0.00%	2.08%	0.00%	NA
Intermediate	90	73.30%	7.80%	18.89%	0.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1111310432	G -> A	LOC_Os11g19620.1	missense_variant ; p.Ala524Thr; MODERATE	nonsynonymous_codon ; A524T	Average:17.182; most accessible tissue: Zhenshan97 panicle, score: 28.447	benign	0.822	DELETERIOUS	0.04
vg1111310432	G -> DEL	LOC_Os11g19620.1	N	frameshift_variant	Average:17.182; most accessible tissue: Zhenshan97 panicle, score: 28.447	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1111310432	1.12E-06	NA	mr1139	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