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Detailed information for vg0114132106:

Variant ID: vg0114132106 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 14132106
Reference Allele: C	Alternative Allele: T,A
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ACAGCAGCATGATGAGCTGACTGAAGCTTTGGGAACTGCAGAACACTCCGGTAGGGTCAGAGGAAAGTCGTGCAGGATGAATTGGAACGTAGGGTTTCCA[C/T,A]
AGGAAGCCCAAAGTTACAAGAAGCGCGACGCCTACAAGGCCAAGATGCGCCAGGAAATCACAGATCAAGTCATACAACAAGTCACCCAACAATTCTACAG

Reverse complement sequence

CTGTAGAATTGTTGGGTGACTTGTTGTATGACTTGATCTGTGATTTCCTGGCGCATCTTGGCCTTGTAGGCGTCGCGCTTCTTGTAACTTTGGGCTTCCT[G/A,T]
TGGAAACCCTACGTTCCAATTCATCCTGCACGACTTTCCTCTGACCCTACCGGAGTGTTCTGCAGTTCCCAAAGCTTCAGTCAGCTCATCATGCTGCTGT

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	73.60%	5.10%	20.63%	0.57%	A: 0.08%
All Indica	2759	63.90%	6.50%	28.45%	0.94%	A: 0.14%
All Japonica	1512	98.90%	0.40%	0.60%	0.07%	NA
Aus	269	23.40%	15.60%	60.97%	0.00%	NA
Indica I	595	42.70%	4.40%	50.92%	2.02%	NA
Indica II	465	68.60%	4.50%	25.38%	1.51%	NA
Indica III	913	76.60%	8.40%	14.57%	0.11%	A: 0.33%
Indica Intermediate	786	62.60%	7.10%	29.39%	0.76%	A: 0.13%
Temperate Japonica	767	99.70%	0.30%	0.00%	0.00%	NA
Tropical Japonica	504	97.60%	0.80%	1.59%	0.00%	NA
Japonica Intermediate	241	99.20%	0.00%	0.41%	0.41%	NA
VI/Aromatic	96	86.50%	8.30%	5.21%	0.00%	NA
Intermediate	90	81.10%	5.60%	13.33%	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
vg0114132106	C -> T	LOC_Os01g25060.1	stop_gained ; p.Gln276*; HIGH	stop_gained	Average:12.628; most accessible tissue: Callus, score: 41.537	N	N	N	N
vg0114132106	C -> A	LOC_Os01g25060.1	missense_variant ; p.Gln276Lys; MODERATE	nonsynonymous_codon ; Q276K	Average:12.628; most accessible tissue: Callus, score: 41.537	unknown	unknown	TOLERATED	0.27
vg0114132106	C -> DEL	LOC_Os01g25060.1	N	frameshift_variant	Average:12.628; most accessible tissue: Callus, score: 41.537	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0114132106	2.40E-06	9.20E-06	mr1492_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
vg0114132106	8.45E-06	NA	mr1779_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