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Detailed information for vg1124343343:

Variant ID: vg1124343343 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 24343343
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GAGGGTAATTTTATCATCATTGCTAAGGTACTAGAGCAGAAGGTACCATATTTTCTATTGAGAAAATGGTACCTCCTGGTTTATATATATTAAGTATCTC[G/A]
AGGTACCAAAAATTTTACTGTGAAATTTAGATACATCGAGGTACTTTTTCAAGGATACATCGACGTATTTTTTTTCGAATACTGTAAAATTTATCTTCTA

Reverse complement sequence

TAGAAGATAAATTTTACAGTATTCGAAAAAAAATACGTCGATGTATCCTTGAAAAAGTACCTCGATGTATCTAAATTTCACAGTAAAATTTTTGGTACCT[C/T]
GAGATACTTAATATATATAAACCAGGAGGTACCATTTTCTCAATAGAAAATATGGTACCTTCTGCTCTAGTACCTTAGCAATGATGATAAAATTACCCTC

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	83.60%	9.40%	0.11%	6.90%	NA
All Indica	2759	89.10%	10.50%	0.00%	0.40%	NA
All Japonica	1512	71.20%	8.30%	0.26%	20.24%	NA
Aus	269	91.80%	7.80%	0.00%	0.37%	NA
Indica I	595	93.90%	6.10%	0.00%	0.00%	NA
Indica II	465	95.50%	2.60%	0.00%	1.94%	NA
Indica III	913	79.40%	20.60%	0.00%	0.00%	NA
Indica Intermediate	786	92.90%	6.90%	0.00%	0.25%	NA
Temperate Japonica	767	78.90%	14.20%	0.52%	6.39%	NA
Tropical Japonica	504	54.20%	3.00%	0.00%	42.86%	NA
Japonica Intermediate	241	82.20%	0.80%	0.00%	17.01%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	84.40%	5.60%	1.11%	8.89%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1124343343	G -> A	LOC_Os11g40700-LOC_Os11g40720	intergenic_region ; MODIFIER	silent_mutation	Average:36.077; most accessible tissue: Zhenshan97 panicle, score: 67.02	N	N	N	N
vg1124343343	G -> DEL	N	N	silent_mutation	Average:36.077; most accessible tissue: Zhenshan97 panicle, score: 67.02	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1124343343	NA	8.62E-06	mr1030	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
vg1124343343	9.13E-06	NA	mr1172	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
vg1124343343	6.59E-06	NA	mr1245	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
vg1124343343	6.09E-06	1.69E-06	mr1290	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
vg1124343343	NA	1.40E-06	mr1318	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
vg1124343343	NA	8.82E-06	mr1981	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