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Detailed information for vg0523575244:

Variant ID: vg0523575244 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 23575244
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AGCAAAAATGAAAACCAATACTGCCCCTGGTCCTGACGGCTTGCCAGTTTGCTTTTATAAGGAGTTTTGGGAGCAGTTGAAGGATCAAATCAAAGAGATG[C/T]
TGGATTCTTTGTTTGAGGGGAGACTGGACCTTTGGAGACATAACTATGGGGTGATTACTTCAATTCCAAAGATAAAAGAAGCAAATAACATCAAAGCTTT

Reverse complement sequence

AAAGCTTTGATGTTATTTGCTTCTTTTATCTTTGGAATTGAAGTAATCACCCCATAGTTATGTCTCCAAAGGTCCAGTCTCCCCTCAAACAAAGAATCCA[G/A]
CATCTCTTTGATTTGATCCTTCAACTGCTCCCAAAACTCCTTATAAAAGCAAACTGGCAAGCCGTCAGGACCAGGGGCAGTATTGGTTTTCATTTTTGCT

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	44.10%	5.00%	1.25%	49.68%	NA
All Indica	2759	25.00%	0.10%	1.49%	73.47%	NA
All Japonica	1512	85.30%	14.00%	0.60%	0.07%	NA
Aus	269	3.70%	0.00%	2.23%	94.05%	NA
Indica I	595	10.90%	0.20%	0.50%	88.40%	NA
Indica II	465	37.00%	0.00%	1.08%	61.94%	NA
Indica III	913	25.10%	0.00%	1.86%	73.06%	NA
Indica Intermediate	786	28.40%	0.10%	2.04%	69.47%	NA
Temperate Japonica	767	76.50%	22.80%	0.52%	0.13%	NA
Tropical Japonica	504	95.60%	3.60%	0.79%	0.00%	NA
Japonica Intermediate	241	91.70%	7.90%	0.41%	0.00%	NA
VI/Aromatic	96	44.80%	20.80%	0.00%	34.38%	NA
Intermediate	90	56.70%	2.20%	3.33%	37.78%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0523575244	C -> T	LOC_Os05g40140.1	synonymous_variant ; p.Leu63Leu; LOW	synonymous_codon	Average:10.868; most accessible tissue: Callus, score: 61.787	N	N	N	N
vg0523575244	C -> DEL	LOC_Os05g40140.1	N	frameshift_variant	Average:10.868; most accessible tissue: Callus, score: 61.787	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0523575244	1.07E-06	NA	mr1444_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
vg0523575244	NA	2.53E-06	mr1444_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