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Detailed information for vg0406169990:

Variant ID: vg0406169990 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 6169990
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, T: 0.01, others allele: 0.00, population size: 78. )

Flanking Sequence (100 bp) in Reference Genome:

CCGTTATGCCGGTGAAGCACTTTTCCATAGACCGAACGGCCTCCAAATACCTCTTCATTCCTTCTTCTATTGCCCCAAAGGATTTGTCGACATGGCCTGC[C/T]
ACCAGCTTGTAGTCGGTCCGGATTAGCAAGCGCCGAATTCCTAATGCTTTTGCCTTTCTTAGGCCCAGAAGAATGGCTTCGTATTCTGCCGCGTTGTTGG

Reverse complement sequence

CCAACAACGCGGCAGAATACGAAGCCATTCTTCTGGGCCTAAGAAAGGCAAAAGCATTAGGAATTCGGCGCTTGCTAATCCGGACCGACTACAAGCTGGT[G/A]
GCAGGCCATGTCGACAAATCCTTTGGGGCAATAGAAGAAGGAATGAAGAGGTATTTGGAGGCCGTTCGGTCTATGGAAAAGTGCTTCACCGGCATAACGG

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	89.90%	0.50%	1.80%	7.79%	NA
All Indica	2759	84.10%	0.80%	2.97%	12.14%	NA
All Japonica	1512	98.90%	0.00%	0.00%	1.12%	NA
Aus	269	98.10%	0.00%	0.37%	1.49%	NA
Indica I	595	96.60%	0.00%	0.50%	2.86%	NA
Indica II	465	57.40%	2.40%	8.17%	32.04%	NA
Indica III	913	89.70%	0.00%	0.99%	9.31%	NA
Indica Intermediate	786	83.70%	1.50%	4.07%	10.69%	NA
Temperate Japonica	767	99.70%	0.00%	0.00%	0.26%	NA
Tropical Japonica	504	97.40%	0.00%	0.00%	2.58%	NA
Japonica Intermediate	241	99.20%	0.00%	0.00%	0.83%	NA
VI/Aromatic	96	95.80%	0.00%	1.04%	3.12%	NA
Intermediate	90	87.80%	1.10%	1.11%	10.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0406169990	C -> DEL	LOC_Os04g11300.1	N	frameshift_variant	Average:27.471; most accessible tissue: Zhenshan97 flag leaf, score: 70.425	N	N	N	N
vg0406169990	C -> T	LOC_Os04g11300.1	synonymous_variant ; p.Val437Val; LOW	synonymous_codon	Average:27.471; most accessible tissue: Zhenshan97 flag leaf, score: 70.425	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0406169990	NA	8.54E-06	mr1608	Ind_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0406169990	NA	6.75E-06	mr1626	Ind_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0406169990	NA	9.89E-07	mr1062_2	Ind_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0406169990	NA	1.76E-10	mr1158_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