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Detailed information for vg0612239920:

Variant ID: vg0612239920 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 12239920
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.96, T: 0.02, others allele: 0.00, population size: 45. )

Flanking Sequence (100 bp) in Reference Genome:

CCGTCCATGGCGACCTCAAAGTCGCGCTTGCTTGCATGGAGCAGCGCGCGGACCATCTCGCCGCGGCATCCAAGCCCGCGGGTGGCGACGAGAGGCTCAG[C/T]
ACCTCTGTCCCAGCCGCCCCGAGGCAGCGGATGATCACGTGCGATGAGGTCCCGATCAAGCAGGTTGCCCTGGGCGACGGCCCGTCCAAGACCACACGAA

Reverse complement sequence

TTCGTGTGGTCTTGGACGGGCCGTCGCCCAGGGCAACCTGCTTGATCGGGACCTCATCGCACGTGATCATCCGCTGCCTCGGGGCGGCTGGGACAGAGGT[G/A]
CTGAGCCTCTCGTCGCCACCCGCGGGCTTGGATGCCGCGGCGAGATGGTCCGCGCGCTGCTCCATGCAAGCAAGCGCGACTTTGAGGTCGCCATGGACGG

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	44.80%	7.70%	24.57%	22.92%	NA
All Indica	2759	25.40%	12.00%	38.85%	23.81%	NA
All Japonica	1512	88.20%	0.30%	1.19%	10.32%	NA
Aus	269	11.90%	7.40%	16.36%	64.31%	NA
Indica I	595	18.70%	5.00%	56.97%	19.33%	NA
Indica II	465	29.50%	5.80%	36.77%	27.96%	NA
Indica III	913	29.00%	22.50%	26.94%	21.58%	NA
Indica Intermediate	786	23.80%	8.70%	40.20%	27.35%	NA
Temperate Japonica	767	97.10%	0.00%	1.04%	1.83%	NA
Tropical Japonica	504	73.40%	0.80%	0.79%	25.00%	NA
Japonica Intermediate	241	90.90%	0.00%	2.49%	6.64%	NA
VI/Aromatic	96	6.20%	9.40%	9.38%	75.00%	NA
Intermediate	90	51.10%	1.10%	20.00%	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
vg0612239920	C -> T	LOC_Os06g21180.1	synonymous_variant ; p.Ser502Ser; LOW	synonymous_codon	Average:12.702; most accessible tissue: Zhenshan97 root, score: 25.639	N	N	N	N
vg0612239920	C -> DEL	LOC_Os06g21180.1	N	frameshift_variant	Average:12.702; most accessible tissue: Zhenshan97 root, score: 25.639	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0612239920	2.50E-06	NA	mr1348	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