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Detailed information for vg1109865325:

Variant ID: vg1109865325 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 9865325
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GGTCGTGAAGGAGAAGGTTACAAGGCGAAAGGAAAGCGAAGCCAGGGCGGTTATGGCCGCCGAAGAGGGAGCAGAGCCTTCGGCGCCCATCGCCGAAGAT[G/A]
GAGGAGCGCCATCTGCTTCCGCACCTGCGCCATCACTACCGCCATCGGCTCCTGGCCCCTCCACACAGGTGCCGAACGCGGCTGACATGGCGAAGGCGGC

Reverse complement sequence

GCCGCCTTCGCCATGTCAGCCGCGTTCGGCACCTGTGTGGAGGGGCCAGGAGCCGATGGCGGTAGTGATGGCGCAGGTGCGGAAGCAGATGGCGCTCCTC[C/T]
ATCTTCGGCGATGGGCGCCGAAGGCTCTGCTCCCTCTTCGGCGGCCATAACCGCCCTGGCTTCGCTTTCCTTTCGCCTTGTAACCTTCTCCTTCACGACC

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	44.80%	0.90%	8.82%	45.49%	NA
All Indica	2759	19.60%	1.50%	13.59%	65.31%	NA
All Japonica	1512	96.50%	0.00%	0.40%	3.11%	NA
Aus	269	17.50%	0.00%	8.18%	74.35%	NA
Indica I	595	23.00%	3.00%	17.31%	56.64%	NA
Indica II	465	12.70%	0.90%	11.83%	74.62%	NA
Indica III	913	16.80%	0.30%	11.17%	71.74%	NA
Indica Intermediate	786	24.30%	2.20%	14.63%	58.91%	NA
Temperate Japonica	767	96.90%	0.00%	0.52%	2.61%	NA
Tropical Japonica	504	96.60%	0.00%	0.20%	3.17%	NA
Japonica Intermediate	241	95.00%	0.00%	0.41%	4.56%	NA
VI/Aromatic	96	27.10%	0.00%	6.25%	66.67%	NA
Intermediate	90	50.00%	0.00%	8.89%	41.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1109865325	G -> A	LOC_Os11g17670.1	missense_variant ; p.Gly194Arg; MODERATE	nonsynonymous_codon ; G194R	Average:13.867; most accessible tissue: Callus, score: 25.803	unknown	unknown	TOLERATED	0.15
vg1109865325	G -> DEL	LOC_Os11g17670.1	N	frameshift_variant	Average:13.867; most accessible tissue: Callus, score: 25.803	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1109865325	1.83E-06	NA	mr1458_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
vg1109865325	4.22E-06	NA	mr1866_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
vg1109865325	4.72E-06	NA	mr1866_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
vg1109865325	7.54E-06	NA	mr1916_2	Ind_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251