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Detailed information for vg1123889289:

Variant ID: vg1123889289 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 23889289
Reference Allele: G	Alternative Allele: C
Primary Allele: G	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CTCTAAGTGGGCAAGGTCCTCCTTTTATATCTCAAGGGGATACCACATGCACCATCTCTCTTTTGTGTGTGGGGACTTATCCTATCTTTTTTTCCAACTT[G/C]
ACTTCCCTTCTCTTCATAAATGGACGGAGATTTGTATGGTTGCCATCCGAATGACCTTCTGATGGGACGGCCCATACCTACCTCCACTTCTGTCGGAAGC

Reverse complement sequence

GCTTCCGACAGAAGTGGAGGTAGGTATGGGCCGTCCCATCAGAAGGTCATTCGGATGGCAACCATACAAATCTCCGTCCATTTATGAAGAGAAGGGAAGT[C/G]
AAGTTGGAAAAAAAGATAGGATAAGTCCCCACACACAAAAGAGAGATGGTGCATGTGGTATCCCCTTGAGATATAAAAGGAGGACCTTGCCCACTTAGAG

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	85.40%	4.90%	0.63%	9.06%	NA
All Indica	2759	90.90%	7.80%	0.72%	0.58%	NA
All Japonica	1512	71.80%	0.70%	0.46%	26.98%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	94.30%	3.40%	0.50%	1.85%	NA
Indica II	465	88.40%	10.50%	0.65%	0.43%	NA
Indica III	913	89.30%	9.90%	0.88%	0.00%	NA
Indica Intermediate	786	91.60%	7.30%	0.76%	0.38%	NA
Temperate Japonica	767	75.40%	1.30%	0.26%	23.08%	NA
Tropical Japonica	504	73.20%	0.20%	0.79%	25.79%	NA
Japonica Intermediate	241	57.70%	0.00%	0.41%	41.91%	NA
VI/Aromatic	96	95.80%	2.10%	2.08%	0.00%	NA
Intermediate	90	92.20%	2.20%	1.11%	4.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1123889289	G -> DEL	N	N	silent_mutation	Average:9.023; most accessible tissue: Minghui63 panicle, score: 16.27	N	N	N	N
vg1123889289	G -> C	LOC_Os11g40060.1	upstream_gene_variant ; 493.0bp to feature; MODIFIER	silent_mutation	Average:9.023; most accessible tissue: Minghui63 panicle, score: 16.27	N	N	N	N
vg1123889289	G -> C	LOC_Os11g40070.1	upstream_gene_variant ; 3115.0bp to feature; MODIFIER	silent_mutation	Average:9.023; most accessible tissue: Minghui63 panicle, score: 16.27	N	N	N	N
vg1123889289	G -> C	LOC_Os11g40070.2	upstream_gene_variant ; 3115.0bp to feature; MODIFIER	silent_mutation	Average:9.023; most accessible tissue: Minghui63 panicle, score: 16.27	N	N	N	N
vg1123889289	G -> C	LOC_Os11g40070.3	upstream_gene_variant ; 3115.0bp to feature; MODIFIER	silent_mutation	Average:9.023; most accessible tissue: Minghui63 panicle, score: 16.27	N	N	N	N
vg1123889289	G -> C	LOC_Os11g40060-LOC_Os11g40070	intergenic_region ; MODIFIER	silent_mutation	Average:9.023; most accessible tissue: Minghui63 panicle, score: 16.27	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1123889289	1.81E-06	1.55E-08	mr1672_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