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Detailed information for vg1124745257:

Variant ID: vg1124745257 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 24745257
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 127. )

Flanking Sequence (100 bp) in Reference Genome:

CAACAGGTACAGGGGGGTTTGATAGGTAGCGCTTGAGTGCAAGAAATGCCTCTTCGGCTTCCTGTGTCCATACAAATTTGTCTTGCTTCTTCAGCAGAGC[G/A]
AAGAAGGGTTGTCCTCGTTCTCCCATCCTAGCGATGAACATGCTTAGTGCTGCCATGCATCCGGTTAGCTTTTGTACTTCCTTGAGTCTTGTGGGCGACT

Reverse complement sequence

AGTCGCCCACAAGACTCAAGGAAGTACAAAAGCTAACCGGATGCATGGCAGCACTAAGCATGTTCATCGCTAGGATGGGAGAACGAGGACAACCCTTCTT[C/T]
GCTCTGCTGAAGAAGCAAGACAAATTTGTATGGACACAGGAAGCCGAAGAGGCATTTCTTGCACTCAAGCGCTACCTATCAAACCCCCCTGTACCTGTTG

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	93.20%	1.30%	1.84%	3.60%	NA
All Indica	2759	94.30%	2.00%	2.57%	1.05%	NA
All Japonica	1512	90.60%	0.20%	0.73%	8.47%	NA
Aus	269	96.30%	0.00%	0.00%	3.72%	NA
Indica I	595	90.30%	3.70%	5.38%	0.67%	NA
Indica II	465	88.20%	3.70%	3.66%	4.52%	NA
Indica III	913	99.20%	0.40%	0.22%	0.11%	NA
Indica Intermediate	786	95.40%	1.70%	2.54%	0.38%	NA
Temperate Japonica	767	96.70%	0.40%	0.65%	2.22%	NA
Tropical Japonica	504	81.00%	0.00%	0.79%	18.25%	NA
Japonica Intermediate	241	91.30%	0.00%	0.83%	7.88%	NA
VI/Aromatic	96	97.90%	0.00%	0.00%	2.08%	NA
Intermediate	90	88.90%	4.40%	5.56%	1.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1124745257	G -> A	LOC_Os11g41280.1	synonymous_variant ; p.Phe811Phe; LOW	synonymous_codon	Average:37.586; most accessible tissue: Minghui63 young leaf, score: 51.901	N	N	N	N
vg1124745257	G -> DEL	LOC_Os11g41280.1	N	frameshift_variant	Average:37.586; most accessible tissue: Minghui63 young leaf, score: 51.901	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1124745257	1.48E-07	1.20E-07	mr1123	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
vg1124745257	NA	1.40E-06	mr1191_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
vg1124745257	NA	7.26E-08	mr1662_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
vg1124745257	NA	6.37E-08	mr1662_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