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Detailed information for vg1124348003:

Variant ID: vg1124348003 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 24348003
Reference Allele: C	Alternative Allele: G
Primary Allele: C	Secondary Allele: G

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.97, G: 0.03, others allele: 0.00, population size: 103. )

Flanking Sequence (100 bp) in Reference Genome:

TAGATGTAGCGATGAATATTGCATTATCTCTCGAGGCTTAAATATGAACATAAGTTGAAATTATACAGCCGGATTGATCCAAAAATTAAGCTAAACGTAA[C/G]
TGAACAACATTTGTCAATAACTTCACCAAAATCAGATAAATTTTATATCAAAAATCAGACAAACTGAGAATAATATTTACCCAAAACTTCATCAAAACCG

Reverse complement sequence

CGGTTTTGATGAAGTTTTGGGTAAATATTATTCTCAGTTTGTCTGATTTTTGATATAAAATTTATCTGATTTTGGTGAAGTTATTGACAAATGTTGTTCA[G/C]
TTACGTTTAGCTTAATTTTTGGATCAATCCGGCTGTATAATTTCAACTTATGTTCATATTTAAGCCTCGAGAGATAATGCAATATTCATCGCTACATCTA

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	85.40%	12.90%	0.15%	1.46%	NA
All Indica	2759	84.60%	15.00%	0.07%	0.40%	NA
All Japonica	1512	99.30%	0.70%	0.00%	0.00%	NA
Aus	269	16.70%	59.90%	1.86%	21.56%	NA
Indica I	595	91.30%	8.60%	0.17%	0.00%	NA
Indica II	465	87.50%	12.30%	0.22%	0.00%	NA
Indica III	913	77.20%	22.00%	0.00%	0.77%	NA
Indica Intermediate	786	86.30%	13.20%	0.00%	0.51%	NA
Temperate Japonica	767	99.60%	0.40%	0.00%	0.00%	NA
Tropical Japonica	504	99.60%	0.40%	0.00%	0.00%	NA
Japonica Intermediate	241	97.50%	2.50%	0.00%	0.00%	NA
VI/Aromatic	96	82.30%	17.70%	0.00%	0.00%	NA
Intermediate	90	88.90%	11.10%	0.00%	0.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1124348003	C -> DEL	N	N	silent_mutation	Average:28.781; most accessible tissue: Callus, score: 61.954	N	N	N	N
vg1124348003	C -> G	LOC_Os11g40700-LOC_Os11g40720	intergenic_region ; MODIFIER	silent_mutation	Average:28.781; most accessible tissue: Callus, score: 61.954	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1124348003	1.18E-10	8.06E-12	mr1238	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
vg1124348003	1.54E-07	2.78E-08	mr1309	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
vg1124348003	2.89E-07	2.84E-08	mr1484	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
vg1124348003	NA	1.15E-06	mr1574	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
vg1124348003	NA	1.79E-06	mr1841	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
vg1124348003	3.76E-06	3.76E-06	mr1900	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
vg1124348003	2.69E-07	6.20E-09	mr1238_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
vg1124348003	5.43E-08	1.11E-09	mr1484_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
vg1124348003	NA	1.73E-06	mr1522_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
vg1124348003	1.80E-09	2.70E-12	mr1841_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
vg1124348003	NA	7.50E-06	mr1900_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
vg1124348003	1.67E-08	1.67E-08	mr1945_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