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Detailed information for vg0114807948:

Variant ID: vg0114807948 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 14807948
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.98, T: 0.03, others allele: 0.00, population size: 94. )

Flanking Sequence (100 bp) in Reference Genome:

AGAACGTGGGGTGAGGGGGGCATTGCTTTGTGAGGTTTTCTCAGGTCCAAAGGAAGAGTCGAGTTCCTCACCTGCAAAAATAACTGGTGATAGGCAAAAG[T/C]
GGAGCATGTGCAAGAACCAATGCCGCAAGCAACCTGCGCGCCGCTATCCTGCCGCCCCTATGACCTCACTGCCTCAACCAAAAAAAGGGAGGGGATGCCC

Reverse complement sequence

GGGCATCCCCTCCCTTTTTTTGGTTGAGGCAGTGAGGTCATAGGGGCGGCAGGATAGCGGCGCGCAGGTTGCTTGCGGCATTGGTTCTTGCACATGCTCC[A/G]
CTTTTGCCTATCACCAGTTATTTTTGCAGGTGAGGAACTCGACTCTTCCTTTGGACCTGAGAAAACCTCACAAAGCAATGCCCCCCTCACCCCACGTTCT

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	47.10%	32.10%	3.09%	17.67%	NA
All Indica	2759	68.70%	2.00%	4.46%	24.83%	NA
All Japonica	1512	13.50%	86.40%	0.07%	0.07%	NA
Aus	269	34.60%	29.00%	4.46%	31.97%	NA
Indica I	595	93.90%	1.30%	0.50%	4.20%	NA
Indica II	465	50.80%	3.40%	5.59%	40.22%	NA
Indica III	913	61.30%	0.40%	5.91%	32.31%	NA
Indica Intermediate	786	68.80%	3.40%	5.09%	22.65%	NA
Temperate Japonica	767	5.70%	94.10%	0.13%	0.00%	NA
Tropical Japonica	504	10.50%	89.50%	0.00%	0.00%	NA
Japonica Intermediate	241	44.40%	55.20%	0.00%	0.41%	NA
VI/Aromatic	96	4.20%	38.50%	5.21%	52.08%	NA
Intermediate	90	34.40%	45.60%	5.56%	14.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0114807948	T -> DEL	LOC_Os01g26150.1	N	frameshift_variant	Average:54.849; most accessible tissue: Zhenshan97 flag leaf, score: 88.526	N	N	N	N
vg0114807948	T -> C	LOC_Os01g26150.1	missense_variant ; p.Trp52Arg; MODERATE	nonsynonymous_codon ; W52R	Average:54.849; most accessible tissue: Zhenshan97 flag leaf, score: 88.526	unknown	unknown	DELETERIOUS	0.00

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0114807948	NA	8.84E-10	mr1064	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
vg0114807948	NA	2.65E-09	mr1534	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
vg0114807948	4.75E-06	1.51E-07	mr1719	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
vg0114807948	NA	1.75E-06	mr1745	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
vg0114807948	NA	7.41E-09	mr1064_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
vg0114807948	NA	2.97E-06	mr1113_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
vg0114807948	NA	1.57E-07	mr1519_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
vg0114807948	NA	5.62E-10	mr1745_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