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Detailed information for vg1106690644:

Variant ID: vg1106690644 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 6690644
Reference Allele: A	Alternative Allele: G
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.90, A: 0.10, others allele: 0.00, population size: 57. )

Flanking Sequence (100 bp) in Reference Genome:

AGAGTTCCTCAGGGCATTGAGACCCTTTGCTCTCTGAAGAAACTCTGGCTTCTCAATCTGCACAAATACTTCAAATCTCACTGGACTGATGGAGAAATGC[A/G]
CCAGAAGATGCAGCATGTTCCGGACCTGCGTGTCTAGGAGTGGGATGTTACAACTTACATGTTCCTTCAGTCAAGACTTGTTTGATGCATCTGCATTTCG

Reverse complement sequence

CGAAATGCAGATGCATCAAACAAGTCTTGACTGAAGGAACATGTAAGTTGTAACATCCCACTCCTAGACACGCAGGTCCGGAACATGCTGCATCTTCTGG[T/C]
GCATTTCTCCATCAGTCCAGTGAGATTTGAAGTATTTGTGCAGATTGAGAAGCCAGAGTTTCTTCAGAGAGCAAAGGGTCTCAATGCCCTGAGGAACTCT

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	51.20%	14.20%	0.59%	33.96%	NA
All Indica	2759	35.70%	14.30%	0.72%	49.33%	NA
All Japonica	1512	71.90%	13.70%	0.46%	13.96%	NA
Aus	269	78.40%	20.10%	0.37%	1.12%	NA
Indica I	595	15.80%	11.60%	0.84%	71.76%	NA
Indica II	465	22.80%	6.20%	0.65%	70.32%	NA
Indica III	913	54.70%	18.10%	0.33%	26.94%	NA
Indica Intermediate	786	36.30%	16.70%	1.15%	45.93%	NA
Temperate Japonica	767	74.80%	20.60%	0.65%	3.91%	NA
Tropical Japonica	504	67.30%	6.30%	0.40%	25.99%	NA
Japonica Intermediate	241	72.20%	7.10%	0.00%	20.75%	NA
VI/Aromatic	96	96.90%	1.00%	0.00%	2.08%	NA
Intermediate	90	52.20%	16.70%	0.00%	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
vg1106690644	A -> DEL	LOC_Os11g12020.1	N	frameshift_variant	Average:12.824; most accessible tissue: Callus, score: 68.713	N	N	N	N
vg1106690644	A -> G	LOC_Os11g12020.1	missense_variant ; p.His68Arg; MODERATE	nonsynonymous_codon ; H68C	Average:12.824; most accessible tissue: Callus, score: 68.713	probably damaging	3.097	DELETERIOUS	0.01
vg1106690644	A -> G	LOC_Os11g12020.1	missense_variant ; p.His68Arg; MODERATE	nonsynonymous_codon ; H68R	Average:12.824; most accessible tissue: Callus, score: 68.713	benign	1.493	TOLERATED	0.07

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1106690644	4.30E-07	4.30E-07	mr1419	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