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Detailed information for vg0115837832:

Variant ID: vg0115837832 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 15837832
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TCCTTGCAAAAGAAGCACTCTGCATCCTTAGCGGGCCCTGTCTTTTGAACCTTGGTCTTAGAGTTGCTAGTACTCGTGATCTCATTAGAGTTTAGCTTTC[T/C]
CTTTTGACCACTCTTCTTATTGTTGGGCTTGCGCTTATGCATAACCATCACATGGTTGGAGTTTTTCTTAATGCTTTCCTCGGCAGTCTTTAGCATCCCA

Reverse complement sequence

TGGGATGCTAAAGACTGCCGAGGAAAGCATTAAGAAAAACTCCAACCATGTGATGGTTATGCATAAGCGCAAGCCCAACAATAAGAAGAGTGGTCAAAAG[A/G]
GAAAGCTAAACTCTAATGAGATCACGAGTACTAGCAACTCTAAGACCAAGGTTCAAAAGACAGGGCCCGCTAAGGATGCAGAGTGCTTCTTTTGCAAGGA

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	86.50%	0.20%	6.71%	6.56%	NA
All Indica	2759	78.90%	0.40%	10.47%	10.26%	NA
All Japonica	1512	98.70%	0.00%	0.86%	0.40%	NA
Aus	269	90.70%	0.00%	3.35%	5.95%	NA
Indica I	595	73.80%	0.00%	11.60%	14.62%	NA
Indica II	465	87.70%	0.40%	5.38%	6.45%	NA
Indica III	913	79.40%	0.70%	9.97%	9.97%	NA
Indica Intermediate	786	76.80%	0.40%	13.23%	9.54%	NA
Temperate Japonica	767	99.30%	0.00%	0.39%	0.26%	NA
Tropical Japonica	504	97.60%	0.00%	1.59%	0.79%	NA
Japonica Intermediate	241	99.20%	0.00%	0.83%	0.00%	NA
VI/Aromatic	96	97.90%	0.00%	1.04%	1.04%	NA
Intermediate	90	90.00%	0.00%	5.56%	4.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0115837832	T -> DEL	LOC_Os01g28270.1	N	frameshift_variant	Average:6.471; most accessible tissue: Minghui63 root, score: 13.235	N	N	N	N
vg0115837832	T -> C	LOC_Os01g28270.1	missense_variant ; p.Arg248Gly; MODERATE	nonsynonymous_codon ; R248G	Average:6.471; most accessible tissue: Minghui63 root, score: 13.235	unknown	unknown	TOLERATED	0.07

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0115837832	6.89E-06	6.89E-06	mr1930	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