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Detailed information for vg1113606688:

Variant ID: vg1113606688 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 13606688
Reference Allele: C	Alternative Allele: A
Primary Allele: C	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CTTTGGTGTCTAGCTCGTGCCTACCGTCAAGCGCCTGTGGTCGTCCCCTAGTCTTCCACTGTTTTTCGTTTGTCTTCATGTGTGCTGGGCCTTCGCTGCC[C/A]
ACGTAATAAATTATCTAGTTACGCTTCCGCTTGTTAAACTCTGTATTGTATCAACTTTTGGTGTACCTTCCCTCCTGGGACAAGGAATAATACACGCACG

Reverse complement sequence

CGTGCGTGTATTATTCCTTGTCCCAGGAGGGAAGGTACACCAAAAGTTGATACAATACAGAGTTTAACAAGCGGAAGCGTAACTAGATAATTTATTACGT[G/T]
GGCAGCGAAGGCCCAGCACACATGAAGACAAACGAAAAACAGTGGAAGACTAGGGGACGACCACAGGCGCTTGACGGTAGGCACGAGCTAGACACCAAAG

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	37.50%	0.30%	7.02%	55.18%	NA
All Indica	2759	7.10%	0.50%	8.55%	83.83%	NA
All Japonica	1512	95.40%	0.00%	0.07%	4.50%	NA
Aus	269	3.30%	0.00%	32.71%	63.94%	NA
Indica I	595	10.90%	0.50%	3.53%	85.04%	NA
Indica II	465	7.30%	1.50%	5.59%	85.59%	NA
Indica III	913	1.60%	0.10%	16.32%	81.93%	NA
Indica Intermediate	786	10.30%	0.50%	5.09%	84.10%	NA
Temperate Japonica	767	97.00%	0.00%	0.00%	3.00%	NA
Tropical Japonica	504	92.10%	0.00%	0.20%	7.74%	NA
Japonica Intermediate	241	97.50%	0.00%	0.00%	2.49%	NA
VI/Aromatic	96	88.50%	0.00%	4.17%	7.29%	NA
Intermediate	90	43.30%	0.00%	3.33%	53.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1113606688	C -> A	LOC_Os11g24012.1	upstream_gene_variant ; 2031.0bp to feature; MODIFIER	silent_mutation	Average:16.534; most accessible tissue: Callus, score: 30.458	N	N	N	N
vg1113606688	C -> A	LOC_Os11g24000.1	downstream_gene_variant ; 3894.0bp to feature; MODIFIER	silent_mutation	Average:16.534; most accessible tissue: Callus, score: 30.458	N	N	N	N
vg1113606688	C -> A	LOC_Os11g24006.1	intron_variant ; MODIFIER	silent_mutation	Average:16.534; most accessible tissue: Callus, score: 30.458	N	N	N	N
vg1113606688	C -> DEL	N	N	silent_mutation	Average:16.534; most accessible tissue: Callus, score: 30.458	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1113606688	4.94E-06	4.93E-06	mr1331	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