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Detailed information for vg1112983960:

Variant ID: vg1112983960 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 12983960
Reference Allele: C	Alternative Allele: A
Primary Allele: C	Secondary Allele: A

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.94, C: 0.05, others allele: 0.00, population size: 80. )

Flanking Sequence (100 bp) in Reference Genome:

CCTCGGCCAGACGGGCCTCCAGAGCGGCGTAGCGGCGGGCAAGGGAGCGGTAAGCCTCGAGGAGTAGGTCGTGCTGAGTGGCCTAAGCCTCCGAAAGCTC[C/A]
ACCATGCGAGTCAGCACTGGCTGAGACTCGCTGTACGGACAAGGGTACCTGGCGTCTGCGTGGCCAGAAGGAAGGCGTGGGAGCTGCCAGAAGGCAGAGC

Reverse complement sequence

GCTCTGCCTTCTGGCAGCTCCCACGCCTTCCTTCTGGCCACGCAGACGCCAGGTACCCTTGTCCGTACAGCGAGTCTCAGCCAGTGCTGACTCGCATGGT[G/T]
GAGCTTTCGGAGGCTTAGGCCACTCAGCACGACCTACTCCTCGAGGCTTACCGCTCCCTTGCCCGCCGCTACGCCGCTCTGGAGGCCCGTCTGGCCGAGG

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	48.20%	14.90%	1.23%	35.70%	NA
All Indica	2759	24.60%	16.00%	1.85%	57.48%	NA
All Japonica	1512	95.80%	1.30%	0.07%	2.91%	NA
Aus	269	4.80%	83.60%	0.74%	10.78%	NA
Indica I	595	48.70%	13.30%	0.84%	37.14%	NA
Indica II	465	31.00%	6.20%	1.72%	61.08%	NA
Indica III	913	3.40%	22.50%	1.86%	72.29%	NA
Indica Intermediate	786	27.40%	16.40%	2.67%	53.56%	NA
Temperate Japonica	767	97.30%	2.10%	0.13%	0.52%	NA
Tropical Japonica	504	92.50%	0.60%	0.00%	6.94%	NA
Japonica Intermediate	241	97.90%	0.00%	0.00%	2.07%	NA
VI/Aromatic	96	85.40%	10.40%	1.04%	3.12%	NA
Intermediate	90	58.90%	10.00%	3.33%	27.78%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1112983960	C -> A	LOC_Os11g22580.1	upstream_gene_variant ; 2636.0bp to feature; MODIFIER	silent_mutation	Average:16.558; most accessible tissue: Callus, score: 32.179	N	N	N	N
vg1112983960	C -> A	LOC_Os11g22570.1	intron_variant ; MODIFIER	silent_mutation	Average:16.558; most accessible tissue: Callus, score: 32.179	N	N	N	N
vg1112983960	C -> DEL	N	N	silent_mutation	Average:16.558; most accessible tissue: Callus, score: 32.179	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1112983960	1.61E-07	1.61E-07	mr1344_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