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Detailed information for vg1210552838:

Variant ID: vg1210552838 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 10552838
Reference Allele: A	Alternative Allele: C
Primary Allele: A	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CCTCTTCTGGCATTGGAAGCTCATTGACCTGGGTGGCAAATGCTCGATCAAACACATAGTGATTTTGGTCTTGACTTCCATCCAATGGTAGCTGCGAACT[A/C]
AGCAGCATGCTTGGAATGGACCAAGGGTGTGCCCTGGTTAACTCTCTTGAGGCCAGTGGTGGATTGAGTTGAAAACTTGAGTTACTTGAGGCATACCCGC

Reverse complement sequence

GCGGGTATGCCTCAAGTAACTCAAGTTTTCAACTCAATCCACCACTGGCCTCAAGAGAGTTAACCAGGGCACACCCTTGGTCCATTCCAAGCATGCTGCT[T/G]
AGTTCGCAGCTACCATTGGATGGAAGTCAAGACCAAAATCACTATGTGTTTGATCGAGCATTTGCCACCCAGGTCAATGAGCTTCCAATGCCAGAAGAGG

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	91.50%	0.60%	0.61%	7.28%	NA
All Indica	2759	94.80%	1.00%	0.54%	3.66%	NA
All Japonica	1512	83.40%	0.10%	0.73%	15.81%	NA
Aus	269	98.90%	0.00%	1.12%	0.00%	NA
Indica I	595	91.30%	0.70%	0.67%	7.39%	NA
Indica II	465	94.80%	0.90%	0.43%	3.87%	NA
Indica III	913	98.20%	1.00%	0.55%	0.22%	NA
Indica Intermediate	786	93.50%	1.30%	0.51%	4.71%	NA
Temperate Japonica	767	84.40%	0.10%	0.39%	15.12%	NA
Tropical Japonica	504	86.50%	0.00%	0.99%	12.50%	NA
Japonica Intermediate	241	73.90%	0.00%	1.24%	24.90%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	95.60%	0.00%	0.00%	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
vg1210552838	A -> C	LOC_Os12g18290.1	synonymous_variant ; p.Leu156Leu; LOW	synonymous_codon	Average:32.391; most accessible tissue: Minghui63 flag leaf, score: 69.681	N	N	N	N
vg1210552838	A -> DEL	LOC_Os12g18290.1	N	frameshift_variant	Average:32.391; most accessible tissue: Minghui63 flag leaf, score: 69.681	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1210552838	9.60E-06	5.35E-06	mr1574	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