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Detailed information for vg0207179503:

Variant ID: vg0207179503 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 7179503
Reference Allele: G	Alternative Allele: T
Primary Allele: G	Secondary Allele: T

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 272. )

Flanking Sequence (100 bp) in Reference Genome:

CGGTGGCGATGGTAATGGGCAGTTGACCTGGCAGGCCTCGAGACTCTGGTAGCATTGCCCGTCGCTGACCTCACAACACCAGCAGTTCTTGCAGAGGTCT[G/T]
GTCGCTTTGCACATAGCGGCCCAGGTGGTATGTTGATCTTCTCTCCCAACATGTCACCATTGCTCCGGCCTATTAAATATTAATTAATTAATTACAACGT

Reverse complement sequence

ACGTTGTAATTAATTAATTAATATTTAATAGGCCGGAGCAATGGTGACATGTTGGGAGAGAAGATCAACATACCACCTGGGCCGCTATGTGCAAAGCGAC[C/A]
AGACCTCTGCAAGAACTGCTGGTGTTGTGAGGTCAGCGACGGGCAATGCTACCAGAGTCTCGAGGCCTGCCAGGTCAACTGCCCATTACCATCGCCACCG

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	92.50%	5.80%	1.69%	0.00%	NA
All Indica	2759	88.20%	9.10%	2.72%	0.00%	NA
All Japonica	1512	99.30%	0.70%	0.07%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	95.30%	0.30%	4.37%	0.00%	NA
Indica II	465	62.20%	32.90%	4.95%	0.00%	NA
Indica III	913	98.10%	1.80%	0.11%	0.00%	NA
Indica Intermediate	786	86.60%	10.20%	3.18%	0.00%	NA
Temperate Japonica	767	99.30%	0.70%	0.00%	0.00%	NA
Tropical Japonica	504	99.80%	0.20%	0.00%	0.00%	NA
Japonica Intermediate	241	97.90%	1.70%	0.41%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	81.10%	14.40%	4.44%	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
vg0207179503	G -> T	LOC_Os02g13450.1	missense_variant ; p.Pro51Gln; MODERATE	nonsynonymous_codon ; P51Q	Average:60.321; most accessible tissue: Zhenshan97 young leaf, score: 87.004	unknown	unknown	DELETERIOUS	0.00

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0207179503	NA	4.75E-09	mr1077_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
vg0207179503	NA	2.56E-07	mr1149_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
vg0207179503	NA	4.64E-07	mr1347_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
vg0207179503	NA	5.19E-06	mr1360_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
vg0207179503	NA	6.89E-06	mr1360_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
vg0207179503	1.53E-06	4.40E-07	mr1388_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
vg0207179503	NA	9.68E-06	mr1402_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
vg0207179503	NA	4.18E-06	mr1550_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
vg0207179503	NA	3.72E-06	mr1592_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
vg0207179503	NA	4.27E-06	mr1763_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
vg0207179503	NA	1.37E-07	mr1828_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
vg0207179503	NA	1.57E-06	mr1901_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