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Detailed information for vg1210353594:

Variant ID: vg1210353594 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 10353594
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CATGTGAATAAACTATATGAATGTATGAAATTGATTAGTAATTAAACAAGAAATCGATACGTAATGAAATTTTGAATTTATTTGTACATACATCGAGCTC[T/C]
CTTGTGGTGATGATTTGGTCTACAAGGCAGTGGCAATACTCGCACACGTAATAGCCGCACAAGTTAGTTCCCCGCTTTTGCTTTGCGCACTACAAATAAA

Reverse complement sequence

TTTATTTGTAGTGCGCAAAGCAAAAGCGGGGAACTAACTTGTGCGGCTATTACGTGTGCGAGTATTGCCACTGCCTTGTAGACCAAATCATCACCACAAG[A/G]
GAGCTCGATGTATGTACAAATAAATTCAAAATTTCATTACGTATCGATTTCTTGTTTAATTACTAATCAATTTCATACATTCATATAGTTTATTCACATG

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	75.60%	0.20%	7.81%	16.40%	NA
All Indica	2759	67.70%	0.30%	12.07%	19.86%	NA
All Japonica	1512	96.90%	0.00%	0.13%	2.98%	NA
Aus	269	45.70%	0.00%	7.81%	46.47%	NA
Indica I	595	73.80%	0.00%	4.87%	21.34%	NA
Indica II	465	68.40%	0.00%	12.69%	18.92%	NA
Indica III	913	65.90%	0.80%	16.32%	16.98%	NA
Indica Intermediate	786	64.90%	0.30%	12.21%	22.65%	NA
Temperate Japonica	767	94.90%	0.00%	0.00%	5.08%	NA
Tropical Japonica	504	98.60%	0.00%	0.40%	0.99%	NA
Japonica Intermediate	241	99.60%	0.00%	0.00%	0.41%	NA
VI/Aromatic	96	39.60%	0.00%	7.29%	53.12%	NA
Intermediate	90	86.70%	0.00%	6.67%	6.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1210353594	T -> C	LOC_Os12g18010.1	synonymous_variant ; p.Arg758Arg; LOW	synonymous_codon	Average:27.751; most accessible tissue: Minghui63 flag leaf, score: 47.544	N	N	N	N
vg1210353594	T -> DEL	LOC_Os12g18010.1	N	frameshift_variant	Average:27.751; most accessible tissue: Minghui63 flag leaf, score: 47.544	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1210353594	NA	2.82E-07	mr1627	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