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Detailed information for vg0620151422:

Variant ID: vg0620151422 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 20151422
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.91, T: 0.10, others allele: 0.00, population size: 268. )

Flanking Sequence (100 bp) in Reference Genome:

CGATTAAACGGTAAGCATTCTAGTGAAAATAACTTTGTGTTGTGTACCTCAAAATATGGGTGAAATCTTCCTGGGCTACTTGTGATCTTTGGATGGGTTT[C/T]
AGTGCTTCTGATGTATATCAGTTCTTTAGAAATTGAAACAAGTGAATCCAGAACAGCATTGAAGTACCTACTGACCGTCTCACCTGATCGGTAAAACTCA

Reverse complement sequence

TGAGTTTTACCGATCAGGTGAGACGGTCAGTAGGTACTTCAATGCTGTTCTGGATTCACTTGTTTCAATTTCTAAAGAACTGATATACATCAGAAGCACT[G/A]
AAACCCATCCAAAGATCACAAGTAGCCCAGGAAGATTTCACCCATATTTTGAGGTACACAACACAAAGTTATTTTCACTAGAATGCTTACCGTTTAATCG

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	92.80%	3.60%	1.21%	2.31%	NA
All Indica	2759	99.70%	0.30%	0.00%	0.00%	NA
All Japonica	1512	78.60%	10.50%	3.77%	7.08%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	98.50%	1.50%	0.00%	0.00%	NA
Indica III	913	99.90%	0.10%	0.00%	0.00%	NA
Indica Intermediate	786	99.90%	0.10%	0.00%	0.00%	NA
Temperate Japonica	767	88.50%	9.10%	1.30%	1.04%	NA
Tropical Japonica	504	76.80%	6.70%	5.36%	11.11%	NA
Japonica Intermediate	241	51.00%	22.80%	8.30%	17.84%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	93.30%	4.40%	0.00%	2.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0620151422	C -> T	LOC_Os06g34680.1	missense_variant ; p.Glu111Lys; MODERATE	nonsynonymous_codon ; E111K	Average:43.615; most accessible tissue: Zhenshan97 young leaf, score: 73.923	unknown	unknown	TOLERATED	0.14
vg0620151422	C -> DEL	LOC_Os06g34680.1	N	frameshift_variant	Average:43.615; most accessible tissue: Zhenshan97 young leaf, score: 73.923	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0620151422	4.86E-06	NA	mr1082	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
vg0620151422	1.02E-06	NA	mr1103	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
vg0620151422	1.29E-09	NA	mr1082_2	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
vg0620151422	4.32E-07	NA	mr1083_2	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
vg0620151422	3.79E-08	NA	mr1103_2	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
vg0620151422	1.33E-07	NA	mr1104_2	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
vg0620151422	2.08E-06	NA	mr1107_2	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
vg0620151422	1.92E-07	NA	mr1226_2	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
vg0620151422	NA	2.25E-07	mr1408_2	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