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Detailed information for vg1124078152:

Variant ID: vg1124078152 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 24078152
Reference Allele: A	Alternative Allele: G
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ATAATTTGCTCTTCTCGATGCCACAGTGGCAAAACAAAGCCCAGATGACGGTTACGAACTCGACACCGGATTTGAGGTCCTCGGCAAGAGCTGCTGCGTC[A/G]
GAACTGGGAGCAATGTGCACAAGCAAGTGAACCCACACATCAGATAGGATCTCCCAACGACATTTTTGGTCCTCCTTCTTGATGAGTTCATTAGCCAGTA

Reverse complement sequence

TACTGGCTAATGAACTCATCAAGAAGGAGGACCAAAAATGTCGTTGGGAGATCCTATCTGATGTGTGGGTTCACTTGCTTGTGCACATTGCTCCCAGTTC[T/C]
GACGCAGCAGCTCTTGCCGAGGACCTCAAATCCGGTGTCGAGTTCGTAACCGTCATCTGGGCTTTGTTTTGCCACTGTGGCATCGAGAAGAGCAAATTAT

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	37.70%	17.90%	0.85%	43.59%	NA
All Indica	2759	32.80%	3.00%	1.20%	62.96%	NA
All Japonica	1512	45.80%	40.60%	0.26%	13.36%	NA
Aus	269	23.40%	45.00%	1.12%	30.48%	NA
Indica I	595	4.90%	2.50%	1.51%	91.09%	NA
Indica II	465	26.90%	2.60%	0.65%	69.89%	NA
Indica III	913	54.90%	1.10%	0.66%	43.37%	NA
Indica Intermediate	786	31.90%	5.90%	1.91%	60.31%	NA
Temperate Japonica	767	39.20%	52.90%	0.39%	7.43%	NA
Tropical Japonica	504	52.40%	33.70%	0.00%	13.89%	NA
Japonica Intermediate	241	52.70%	15.80%	0.41%	31.12%	NA
VI/Aromatic	96	86.50%	1.00%	0.00%	12.50%	NA
Intermediate	90	42.20%	27.80%	0.00%	30.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1124078152	A -> DEL	LOC_Os11g40390.1	N	frameshift_variant	Average:17.912; most accessible tissue: Callus, score: 60.197	N	N	N	N
vg1124078152	A -> G	LOC_Os11g40390.1	synonymous_variant ; p.Ser348Ser; LOW	synonymous_codon	Average:17.912; most accessible tissue: Callus, score: 60.197	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1124078152	6.13E-06	NA	mr1199_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
vg1124078152	9.54E-06	NA	mr1246_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
vg1124078152	NA	6.02E-06	mr1400_2	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
vg1124078152	NA	8.76E-06	mr1407_2	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
vg1124078152	NA	3.48E-06	mr1462_2	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
vg1124078152	6.64E-06	NA	mr1521_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
vg1124078152	9.38E-07	8.41E-07	mr1609_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
vg1124078152	1.41E-06	NA	mr1763_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
vg1124078152	6.12E-06	NA	mr1767_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
vg1124078152	1.10E-07	1.10E-07	mr1852_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
vg1124078152	NA	6.36E-06	mr1899_2	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
vg1124078152	6.00E-06	NA	mr1906_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
vg1124078152	1.03E-06	3.59E-06	mr1909_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
vg1124078152	3.27E-06	1.96E-06	mr1942_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