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Detailed information for vg1110166732:

Variant ID: vg1110166732 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 10166732
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CAACCAAATCTGAACTCACCAAGTTATTGCAACTCTCACTATCGATTATAGTACGACATGCTCTATCTTTAACCACAAACTTTGTTTTAAATAATTCGTG[A/G]
TACTGCCATTGCTCTGCTTTCTCCATTTGAGAACTTAGCACTTGTTGCACCAAAGTACTGTCATCACGTGCACCTTGTTGGTATCGCTGATTTCGAGCGC

Reverse complement sequence

GCGCTCGAAATCAGCGATACCAACAAGGTGCACGTGATGACAGTACTTTGGTGCAACAAGTGCTAAGTTCTCAAATGGAGAAAGCAGAGCAATGGCAGTA[T/C]
CACGAATTATTTAAAACAAAGTTTGTGGTTAAAGATAGAGCATGTCGTACTATAATCGATAGTGAGAGTTGCAATAACTTGGTGAGTTCAGATTTGGTTG

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	63.30%	0.30%	3.66%	32.71%	NA
All Indica	2759	47.80%	0.40%	4.75%	47.12%	NA
All Japonica	1512	98.50%	0.10%	0.00%	1.39%	NA
Aus	269	17.80%	0.00%	13.75%	68.40%	NA
Indica I	595	68.90%	0.00%	1.85%	29.24%	NA
Indica II	465	14.00%	1.70%	12.90%	71.40%	NA
Indica III	913	52.10%	0.00%	1.97%	45.89%	NA
Indica Intermediate	786	46.70%	0.30%	5.34%	47.71%	NA
Temperate Japonica	767	97.90%	0.00%	0.00%	2.09%	NA
Tropical Japonica	504	98.80%	0.40%	0.00%	0.79%	NA
Japonica Intermediate	241	99.60%	0.00%	0.00%	0.41%	NA
VI/Aromatic	96	89.60%	0.00%	0.00%	10.42%	NA
Intermediate	90	56.70%	3.30%	5.56%	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
vg1110166732	A -> DEL	LOC_Os11g18080.1	N	frameshift_variant	Average:15.708; most accessible tissue: Zhenshan97 flag leaf, score: 36.135	N	N	N	N
vg1110166732	A -> G	LOC_Os11g18080.1	synonymous_variant ; p.Tyr74Tyr; LOW	synonymous_codon	Average:15.708; most accessible tissue: Zhenshan97 flag leaf, score: 36.135	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1110166732	6.60E-06	4.45E-06	mr1386_2	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