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Detailed information for vg1124348408:

Variant ID: vg1124348408 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 24348408
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.01, others allele: 0.00, population size: 259. )

Flanking Sequence (100 bp) in Reference Genome:

ATTGCGAGGTGATACATGCGAAGTCAACAATAGGGATCGAGGCCGAGACAGTGCAAGTGATACAAGTCAATGCTACGAGATGCTGGTGATGCAAATAGGG[G/A]
CCAAGCTAGACAACTAATCTGGGAGAAGTTCATTGGAGTTGCATAGGAAATTCTCAACAGCCTACGCACGGGTCGATGGCCACATGCCACATCCACATGC

Reverse complement sequence

GCATGTGGATGTGGCATGTGGCCATCGACCCGTGCGTAGGCTGTTGAGAATTTCCTATGCAACTCCAATGAACTTCTCCCAGATTAGTTGTCTAGCTTGG[C/T]
CCCTATTTGCATCACCAGCATCTCGTAGCATTGACTTGTATCACTTGCACTGTCTCGGCCTCGATCCCTATTGTTGACTTCGCATGTATCACCTCGCAAT

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	93.10%	5.30%	0.30%	1.33%	NA
All Indica	2759	95.60%	3.70%	0.18%	0.51%	NA
All Japonica	1512	99.70%	0.30%	0.00%	0.00%	NA
Aus	269	31.20%	47.60%	2.97%	18.22%	NA
Indica I	595	98.50%	0.20%	0.67%	0.67%	NA
Indica II	465	90.30%	9.70%	0.00%	0.00%	NA
Indica III	913	98.60%	0.70%	0.00%	0.77%	NA
Indica Intermediate	786	93.00%	6.50%	0.13%	0.38%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	99.80%	0.20%	0.00%	0.00%	NA
Japonica Intermediate	241	98.30%	1.70%	0.00%	0.00%	NA
VI/Aromatic	96	91.70%	8.30%	0.00%	0.00%	NA
Intermediate	90	92.20%	6.70%	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
vg1124348408	G -> A	LOC_Os11g40700-LOC_Os11g40720	intergenic_region ; MODIFIER	silent_mutation	Average:45.061; most accessible tissue: Zhenshan97 young leaf, score: 75.397	N	N	N	N
vg1124348408	G -> DEL	N	N	silent_mutation	Average:45.061; most accessible tissue: Zhenshan97 young leaf, score: 75.397	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1124348408	2.85E-06	NA	mr1238	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
vg1124348408	NA	4.56E-06	mr1262	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
vg1124348408	1.11E-06	NA	mr1309	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
vg1124348408	1.24E-07	NA	mr1841	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
vg1124348408	7.16E-06	NA	mr1841_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