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Detailed information for vg0604502626:

Variant ID: vg0604502626 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 4502626
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 124. )

Flanking Sequence (100 bp) in Reference Genome:

ACGAAGCCGGTGTAGAAGAAGAAGCCGATGGTGGCAAGCCAGAGATCCCTGGTCAGTGGCTTCACGAAAATCCATTGGATTGGCTTGGAGTCGTTCTCCT[C/T]
CGGCACCAGCAGCGACACACCGGACGACGTGTATGGCATCGTGAATTCCACGAGGTTTTCTCGGTCGGCTGTGATGGTCACGTCGCCCACTGCTGCGCTG

Reverse complement sequence

CAGCGCAGCAGTGGGCGACGTGACCATCACAGCCGACCGAGAAAACCTCGTGGAATTCACGATGCCATACACGTCGTCCGGTGTGTCGCTGCTGGTGCCG[G/A]
AGGAGAACGACTCCAAGCCAATCCAATGGATTTTCGTGAAGCCACTGACCAGGGATCTCTGGCTTGCCACCATCGGCTTCTTCTTCTACACCGGCTTCGT

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	89.30%	5.10%	4.27%	1.33%	NA
All Indica	2759	93.40%	5.30%	1.30%	0.07%	NA
All Japonica	1512	80.80%	5.40%	9.99%	3.77%	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	70.30%	25.20%	4.09%	0.43%	NA
Indica III	913	99.30%	0.20%	0.44%	0.00%	NA
Indica Intermediate	786	95.20%	3.30%	1.53%	0.00%	NA
Temperate Japonica	767	84.00%	0.80%	9.13%	6.13%	NA
Tropical Japonica	504	76.20%	12.90%	10.52%	0.40%	NA
Japonica Intermediate	241	80.50%	4.60%	11.62%	3.32%	NA
VI/Aromatic	96	79.20%	5.20%	13.54%	2.08%	NA
Intermediate	90	84.40%	11.10%	2.22%	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
vg0604502626	C -> T	LOC_Os06g08930.1	missense_variant ; p.Glu14Lys; MODERATE	nonsynonymous_codon ; E14K	Average:22.594; most accessible tissue: Zhenshan97 root, score: 38.035	benign	1.115	TOLERATED	0.45
vg0604502626	C -> DEL	LOC_Os06g08930.1	N	frameshift_variant	Average:22.594; most accessible tissue: Zhenshan97 root, score: 38.035	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0604502626	3.61E-06	NA	mr1115	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
vg0604502626	NA	3.73E-15	mr1141	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
vg0604502626	NA	3.18E-06	mr1621	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
vg0604502626	2.57E-06	2.56E-06	mr1621	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
vg0604502626	NA	6.41E-10	mr1903	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
vg0604502626	NA	5.30E-12	mr1907	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
vg0604502626	NA	5.47E-11	mr1934	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
vg0604502626	NA	1.16E-06	mr1951	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
vg0604502626	NA	3.46E-14	mr1141_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
vg0604502626	NA	5.26E-06	mr1425_2	Jap_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
vg0604502626	NA	6.43E-06	mr1667_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
vg0604502626	NA	9.97E-11	mr1889_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
vg0604502626	NA	7.95E-07	mr1896_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
vg0604502626	NA	1.01E-10	mr1907_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
vg0604502626	NA	1.98E-11	mr1934_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