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Detailed information for vg0218106658:

Variant ID: vg0218106658 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 18106658
Reference Allele: C	Alternative Allele: T
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.75, T: 0.26, others allele: 0.00, population size: 204. )

Flanking Sequence (100 bp) in Reference Genome:

ATTGCATATCCATCTTTGAGATAATCGATACAGCACTCGACAACCTCTTCAGTACTATAACCCTCAACCATTGATCCCTCTGGATGTGCACGATTTCGAA[C/T]
GTAACCCTTCAAAACTGCCATGTAACGCTCGTATGACCACATTTGATGGAGATACAATGGGCCAAGTGCAACCATCTGCGGCACTATGTGAACAATGAGG

Reverse complement sequence

CCTCATTGTTCACATAGTGCCGCAGATGGTTGCACTTGGCCCATTGTATCTCCATCAAATGTGGTCATACGAGCGTTACATGGCAGTTTTGAAGGGTTAC[G/A]
TTCGAAATCGTGCACATCCAGAGGGATCAATGGTTGAGGGTTATAGTACTGAAGAGGTTGTCGAGTGCTGTATCGATTATCTCAAAGATGGATATGCAAT

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	41.90%	24.10%	21.92%	12.04%	NA
All Indica	2759	40.40%	5.10%	34.69%	19.79%	NA
All Japonica	1512	34.00%	62.90%	2.31%	0.79%	NA
Aus	269	84.80%	3.70%	10.78%	0.74%	NA
Indica I	595	31.80%	3.90%	41.18%	23.19%	NA
Indica II	465	45.60%	5.60%	22.80%	26.02%	NA
Indica III	913	47.00%	6.00%	35.82%	11.17%	NA
Indica Intermediate	786	36.40%	4.60%	35.50%	23.54%	NA
Temperate Japonica	767	4.30%	94.50%	0.52%	0.65%	NA
Tropical Japonica	504	77.20%	17.90%	4.17%	0.79%	NA
Japonica Intermediate	241	38.20%	56.40%	4.15%	1.24%	NA
VI/Aromatic	96	81.20%	17.70%	1.04%	0.00%	NA
Intermediate	90	48.90%	25.60%	15.56%	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
vg0218106658	C -> T	LOC_Os02g30400.1	missense_variant ; p.Val518Ile; MODERATE	nonsynonymous_codon ; V518I	Average:19.263; most accessible tissue: Zhenshan97 flag leaf, score: 28.494	benign	0.622	TOLERATED	0.06
vg0218106658	C -> DEL	LOC_Os02g30400.1	N	frameshift_variant	Average:19.263; most accessible tissue: Zhenshan97 flag leaf, score: 28.494	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0218106658	NA	1.18E-09	mr1018	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
vg0218106658	NA	5.08E-09	mr1019	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
vg0218106658	NA	2.47E-07	mr1022	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
vg0218106658	7.95E-07	3.70E-15	mr1079	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
vg0218106658	NA	1.75E-15	mr1142	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
vg0218106658	7.91E-06	1.47E-15	mr1489	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
vg0218106658	NA	1.49E-14	mr1491	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
vg0218106658	NA	1.37E-06	mr1629	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
vg0218106658	NA	1.68E-16	mr1769	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
vg0218106658	NA	1.23E-13	mr1778	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
vg0218106658	NA	8.88E-06	mr1780	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
vg0218106658	NA	2.83E-06	mr1498_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
vg0218106658	NA	2.90E-14	mr1769_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
vg0218106658	NA	3.09E-06	mr1793_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
vg0218106658	NA	2.38E-09	mr1916_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