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Detailed information for vg0713264535:

Variant ID: vg0713264535 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 13264535
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GTGCATGACCTTCTGCCTTGCAAAACTTGCAAAGGAACTTACCAGCAGAGTTCTGACCTGCTGGAATCTGAGTTTTGCCCTTATGGGCACCATTAGAAGC[C/T]
TGAGTGGAAGGAGTGTTGGGCTTCTTCTTCTTGTTTTGGGAGTTGCTGGACTCCCCTTGATAGAACTTCTTCTTACTGCCCTTAGCACCATGAAGGAGGT

Reverse complement sequence

ACCTCCTTCATGGTGCTAAGGGCAGTAAGAAGAAGTTCTATCAAGGGGAGTCCAGCAACTCCCAAAACAAGAAGAAGAAGCCCAACACTCCTTCCACTCA[G/A]
GCTTCTAATGGTGCCCATAAGGGCAAAACTCAGATTCCAGCAGGTCAGAACTCTGCTGGTAAGTTCCTTTGCAAGTTTTGCAAGGCAGAAGGTCATGCAC

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	84.60%	8.60%	4.99%	1.82%	NA
All Indica	2759	78.90%	13.70%	6.45%	0.98%	NA
All Japonica	1512	93.80%	1.30%	1.52%	3.37%	NA
Aus	269	89.60%	3.00%	5.20%	2.23%	NA
Indica I	595	91.90%	1.20%	5.55%	1.34%	NA
Indica II	465	88.00%	3.40%	5.59%	3.01%	NA
Indica III	913	63.60%	28.50%	7.78%	0.11%	NA
Indica Intermediate	786	81.40%	12.00%	6.11%	0.51%	NA
Temperate Japonica	767	95.30%	0.30%	0.65%	3.78%	NA
Tropical Japonica	504	96.20%	1.00%	2.38%	0.40%	NA
Japonica Intermediate	241	84.20%	5.00%	2.49%	8.30%	NA
VI/Aromatic	96	83.30%	0.00%	15.62%	1.04%	NA
Intermediate	90	91.10%	1.10%	6.67%	1.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0713264535	C -> DEL	LOC_Os07g23480.1	N	frameshift_variant	Average:28.995; most accessible tissue: Minghui63 root, score: 43.505	N	N	N	N
vg0713264535	C -> T	LOC_Os07g23480.1	synonymous_variant ; p.Gln970Gln; LOW	synonymous_codon	Average:28.995; most accessible tissue: Minghui63 root, score: 43.505	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0713264535	1.82E-06	1.07E-07	mr1662	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
vg0713264535	NA	3.87E-06	mr1662_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