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Detailed information for vg1121909998:

Variant ID: vg1121909998 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 21909998
Reference Allele: G	Alternative Allele: C
Primary Allele: G	Secondary Allele: C

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 222. )

Flanking Sequence (100 bp) in Reference Genome:

AGTACTAGCTGCTTCTGATAATTATGGTATCATTACTCTTTTATGTGAGACAATTTTGTCACAGTTATTCACTTATTCTGCTTTATCAAATTTTCTTTAA[G/C]
GATTTGGTTGCCGAAATTATGTTTTGGAAAAATTCGGAGCAATCCTATGATCAAGCGAATAGATCTTACATGTTTCTGCAGTTCGGCAGTCCGCACCTGA

Reverse complement sequence

TCAGGTGCGGACTGCCGAACTGCAGAAACATGTAAGATCTATTCGCTTGATCATAGGATTGCTCCGAATTTTTCCAAAACATAATTTCGGCAACCAAATC[C/G]
TTAAAGAAAATTTGATAAAGCAGAATAAGTGAATAACTGTGACAAAATTGTCTCACATAAAAGAGTAATGATACCATAATTATCAGAAGCAGCTAGTACT

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	92.10%	1.30%	1.12%	5.50%	NA
All Indica	2759	94.90%	0.90%	0.04%	4.24%	NA
All Japonica	1512	94.30%	0.90%	3.31%	1.46%	NA
Aus	269	69.90%	7.10%	0.37%	22.68%	NA
Indica I	595	85.20%	0.00%	0.00%	14.79%	NA
Indica II	465	98.30%	0.00%	0.00%	1.72%	NA
Indica III	913	99.10%	0.80%	0.00%	0.11%	NA
Indica Intermediate	786	95.20%	2.20%	0.13%	2.54%	NA
Temperate Japonica	767	96.70%	0.30%	0.78%	2.22%	NA
Tropical Japonica	504	90.10%	1.60%	7.94%	0.40%	NA
Japonica Intermediate	241	95.40%	1.70%	1.66%	1.24%	NA
VI/Aromatic	96	49.00%	1.00%	1.04%	48.96%	NA
Intermediate	90	82.20%	3.30%	0.00%	14.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1121909998	G -> DEL	N	N	silent_mutation	Average:55.998; most accessible tissue: Callus, score: 82.021	N	N	N	N
vg1121909998	G -> C	LOC_Os11g37100.1	downstream_gene_variant ; 731.0bp to feature; MODIFIER	silent_mutation	Average:55.998; most accessible tissue: Callus, score: 82.021	N	N	N	N
vg1121909998	G -> C	LOC_Os11g37120.1	downstream_gene_variant ; 2914.0bp to feature; MODIFIER	silent_mutation	Average:55.998; most accessible tissue: Callus, score: 82.021	N	N	N	N
vg1121909998	G -> C	LOC_Os11g37110.1	intron_variant ; MODIFIER	silent_mutation	Average:55.998; most accessible tissue: Callus, score: 82.021	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1121909998	NA	3.89E-06	mr1045	Jap_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
vg1121909998	NA	4.68E-07	mr1668	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
vg1121909998	3.97E-06	5.16E-07	mr1991	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