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Detailed information for vg0112185618:

Variant ID: vg0112185618 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 12185618
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.01, others allele: 0.00, population size: 340. )

Flanking Sequence (100 bp) in Reference Genome:

TCATTGGGATCATCACGGATTACTTACGAGGGATTGAAGATGCAGAAGTGCGGCACGACCGAGAAAATGTGCATCACATGCTCCATCTCTATCACTGTTG[C/T]
TTTGTTCAGCCACTCGAACTGCCAAGAAATGCAAACGAAGAAGGTGGAAATGCGAATAATATTGGTAATCCCTTCCTGTTCTTGCCCAAGATGATCCCAT

Reverse complement sequence

ATGGGATCATCTTGGGCAAGAACAGGAAGGGATTACCAATATTATTCGCATTTCCACCTTCTTCGTTTGCATTTCTTGGCAGTTCGAGTGGCTGAACAAA[G/A]
CAACAGTGATAGAGATGGAGCATGTGATGCACATTTTCTCGGTCGTGCCGCACTTCTGCATCTTCAATCCCTCGTAAGTAATCCGTGATGATCCCAATGA

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	93.00%	2.30%	1.08%	3.60%	NA
All Indica	2759	98.70%	0.00%	0.22%	1.12%	NA
All Japonica	1512	80.90%	7.10%	2.91%	9.13%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	99.80%	0.00%	0.17%	0.00%	NA
Indica II	465	97.00%	0.00%	0.65%	2.37%	NA
Indica III	913	99.50%	0.00%	0.00%	0.55%	NA
Indica Intermediate	786	97.80%	0.00%	0.25%	1.91%	NA
Temperate Japonica	767	81.00%	9.10%	4.17%	5.74%	NA
Tropical Japonica	504	80.40%	1.20%	1.79%	16.67%	NA
Japonica Intermediate	241	81.70%	12.90%	1.24%	4.15%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	93.30%	4.40%	1.11%	1.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0112185618	C -> T	LOC_Os01g21710.1	synonymous_variant ; p.Cys254Cys; LOW	synonymous_codon	Average:47.144; most accessible tissue: Zhenshan97 young leaf, score: 72.747	N	N	N	N
vg0112185618	C -> DEL	LOC_Os01g21710.1	N	frameshift_variant	Average:47.144; most accessible tissue: Zhenshan97 young leaf, score: 72.747	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0112185618	2.75E-06	2.75E-06	mr1803	Jap_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