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Detailed information for vg0506796325:

Variant ID: vg0506796325 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 6796325
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TACAACGAGCCTTGGAGATGATGGTTCTGTTCATGCGCTCAGCCACACCATTCTGCTGTGGAGTGTACGGGATGGTGTGATGCATAACGATGCCTTCCTT[C/T]
CTACAATAATCATCAAAAGCATCCGAACAAAATCCACCACCATTGTCAGTGCGAAGTACTTTTACCTCCTTTTCAGTTTGCCTTTTTATCATGACTTTCC

Reverse complement sequence

GGAAAGTCATGATAAAAAGGCAAACTGAAAAGGAGGTAAAAGTACTTCGCACTGACAATGGTGGTGGATTTTGTTCGGATGCTTTTGATGATTATTGTAG[G/A]
AAGGAAGGCATCGTTATGCATCACACCATCCCGTACACTCCACAGCAGAATGGTGTGGCTGAGCGCATGAACAGAACCATCATCTCCAAGGCTCGTTGTA

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	37.70%	5.20%	23.40%	33.66%	NA
All Indica	2759	5.20%	4.50%	34.69%	55.64%	NA
All Japonica	1512	95.20%	0.50%	3.57%	0.73%	NA
Aus	269	21.20%	41.30%	26.02%	11.52%	NA
Indica I	595	2.00%	3.20%	12.44%	82.35%	NA
Indica II	465	4.30%	5.20%	48.39%	42.15%	NA
Indica III	913	7.60%	3.90%	43.15%	45.35%	NA
Indica Intermediate	786	5.30%	5.70%	33.59%	55.34%	NA
Temperate Japonica	767	98.30%	0.00%	0.65%	1.04%	NA
Tropical Japonica	504	94.80%	0.80%	3.97%	0.40%	NA
Japonica Intermediate	241	86.30%	1.20%	12.03%	0.41%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	53.30%	3.30%	27.78%	15.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0506796325	C -> T	LOC_Os05g11940.1	synonymous_variant ; p.Arg464Arg; LOW	synonymous_codon	Average:22.774; most accessible tissue: Callus, score: 30.51	N	N	N	N
vg0506796325	C -> DEL	LOC_Os05g11940.1	N	frameshift_variant	Average:22.774; most accessible tissue: Callus, score: 30.51	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0506796325	NA	1.33E-26	mr1309	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
vg0506796325	7.06E-07	1.88E-07	mr1310	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
vg0506796325	NA	9.66E-08	mr1335_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
vg0506796325	NA	1.60E-22	mr1386_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
vg0506796325	NA	1.06E-32	mr1632_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