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Detailed information for vg1124335591:

Variant ID: vg1124335591 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 24335591
Reference Allele: G	Alternative Allele: C
Primary Allele: G	Secondary Allele: C

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.94, C: 0.06, others allele: 0.00, population size: 218. )

Flanking Sequence (100 bp) in Reference Genome:

ATGAACACATAAATAAACAGATAACACAAATAGAGCCCGCACATTGCCGTAGATTTTTTAAGATACAGGAAGCTTTTATTGAACCCAGCCAACAACTATA[G/C]
CAAGAAAATACAAAAGCACTGAAAGCCCGAGCGTCACCGTAAACGATTAGATGGATCCAACTCAAGGCATGCAGGCTTGGAAGATATGGTGGTCCTTGTA

Reverse complement sequence

TACAAGGACCACCATATCTTCCAAGCCTGCATGCCTTGAGTTGGATCCATCTAATCGTTTACGGTGACGCTCGGGCTTTCAGTGCTTTTGTATTTTCTTG[C/G]
TATAGTTGTTGGCTGGGTTCAATAAAAGCTTCCTGTATCTTAAAAAATCTACGGCAATGTGCGGGCTCTATTTGTGTTATCTGTTTATTTATGTGTTCAT

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	83.90%	14.50%	0.15%	1.50%	NA
All Indica	2759	86.00%	13.40%	0.00%	0.58%	NA
All Japonica	1512	91.30%	8.60%	0.07%	0.00%	NA
Aus	269	19.00%	58.70%	1.86%	20.45%	NA
Indica I	595	93.60%	6.40%	0.00%	0.00%	NA
Indica II	465	88.20%	11.60%	0.00%	0.22%	NA
Indica III	913	80.90%	18.30%	0.00%	0.77%	NA
Indica Intermediate	786	84.70%	14.20%	0.00%	1.02%	NA
Temperate Japonica	767	96.90%	3.00%	0.13%	0.00%	NA
Tropical Japonica	504	84.30%	15.70%	0.00%	0.00%	NA
Japonica Intermediate	241	88.40%	11.60%	0.00%	0.00%	NA
VI/Aromatic	96	83.30%	16.70%	0.00%	0.00%	NA
Intermediate	90	87.80%	11.10%	1.11%	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
vg1124335591	G -> DEL	N	N	silent_mutation	Average:43.521; most accessible tissue: Minghui63 panicle, score: 62.157	N	N	N	N
vg1124335591	G -> C	LOC_Os11g40700-LOC_Os11g40720	intergenic_region ; MODIFIER	silent_mutation	Average:43.521; most accessible tissue: Minghui63 panicle, score: 62.157	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1124335591	1.26E-09	2.27E-11	mr1238	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
vg1124335591	2.19E-07	3.12E-08	mr1309	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
vg1124335591	NA	4.13E-06	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
vg1124335591	NA	6.88E-07	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
vg1124335591	1.38E-06	1.38E-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
vg1124335591	1.25E-07	1.98E-08	mr1238_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
vg1124335591	9.53E-08	9.05E-09	mr1484_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
vg1124335591	1.04E-08	1.77E-10	mr1841_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
vg1124335591	1.49E-07	1.49E-07	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