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Detailed information for vg0434493414:

Variant ID: vg0434493414 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 34493414
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: 350. )

Flanking Sequence (100 bp) in Reference Genome:

TAAAACCAATAACATCGATTTATTAAAATTTGCTCTAGATTCAGTGGATAAACTTACTTGTTAATGTCATCTGAAGAATAACCAGTAACACCACCAAATA[C/T]
GACAAGCACATAATTCACATCCAGTGACTGCATTATCTCATACGCTTCATCTTCATAGGATGACATTGCACGCCCAACTGTAGCTATATGTGTATTATTC

Reverse complement sequence

GAATAATACACATATAGCTACAGTTGGGCGTGCAATGTCATCCTATGAAGATGAAGCGTATGAGATAATGCAGTCACTGGATGTGAATTATGTGCTTGTC[G/A]
TATTTGGTGGTGTTACTGGTTATTCTTCAGATGACATTAACAAGTAAGTTTATCCACTGAATCTAGAGCAAATTTTAATAAATCGATGTTATTGGTTTTA

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	82.20%	16.90%	0.93%	0.00%	NA
All Indica	2759	99.30%	0.70%	0.00%	0.00%	NA
All Japonica	1512	53.20%	44.10%	2.65%	0.00%	NA
Aus	269	74.00%	25.70%	0.37%	0.00%	NA
Indica I	595	99.50%	0.50%	0.00%	0.00%	NA
Indica II	465	99.80%	0.20%	0.00%	0.00%	NA
Indica III	913	99.80%	0.20%	0.00%	0.00%	NA
Indica Intermediate	786	98.50%	1.50%	0.00%	0.00%	NA
Temperate Japonica	767	74.30%	21.60%	4.04%	0.00%	NA
Tropical Japonica	504	12.50%	86.50%	0.99%	0.00%	NA
Japonica Intermediate	241	71.40%	27.00%	1.66%	0.00%	NA
VI/Aromatic	96	75.00%	24.00%	1.04%	0.00%	NA
Intermediate	90	75.60%	22.20%	2.22%	0.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0434493414	C -> T	LOC_Os04g57890.1	missense_variant ; p.Val604Ile; MODERATE	nonsynonymous_codon ; V604I	Average:46.727; most accessible tissue: Minghui63 flower, score: 56.663	benign	0.877	TOLERATED	1.00

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0434493414	NA	1.67E-09	mr1151	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
vg0434493414	NA	1.64E-15	mr1164	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
vg0434493414	NA	1.09E-07	mr1164	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
vg0434493414	NA	1.47E-07	mr1249	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
vg0434493414	NA	5.66E-20	mr1580	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
vg0434493414	NA	9.39E-06	mr1992	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
vg0434493414	NA	1.27E-08	mr1084_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
vg0434493414	NA	1.81E-11	mr1097_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
vg0434493414	3.55E-06	1.80E-22	mr1164_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
vg0434493414	NA	5.30E-08	mr1164_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
vg0434493414	NA	6.66E-08	mr1205_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
vg0434493414	NA	9.26E-06	mr1206_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
vg0434493414	NA	1.76E-06	mr1405_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
vg0434493414	NA	4.54E-14	mr1521_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
vg0434493414	NA	1.90E-08	mr1668_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