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Detailed information for vg0116963933:

Variant ID: vg0116963933 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 16963933
Reference Allele: T	Alternative Allele: A
Primary Allele: T	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CTTTTCGGGCGCCTTCCCAGCCAGCGAGCAAGCGACCAGCTGCATTCGGAGCTTCTGCGGCACCAAAACCATCTCCACCACAACCAGCAGAGTCAGGTAA[T/A]
GGTTCTTCGCAGGTACCCGCCAAGAGTGCCTCATCTGTCGCCTCGACGGGACGCATTCAGTGCCACCGTTGCCAAGGGTTTGGGCATGTGCAGAAAGATT

Reverse complement sequence

AATCTTTCTGCACATGCCCAAACCCTTGGCAACGGTGGCACTGAATGCGTCCCGTCGAGGCGACAGATGAGGCACTCTTGGCGGGTACCTGCGAAGAACC[A/T]
TTACCTGACTCTGCTGGTTGTGGTGGAGATGGTTTTGGTGCCGCAGAAGCTCCGAATGCAGCTGGTCGCTTGCTCGCTGGCTGGGAAGGCGCCCGAAAAG

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	41.60%	8.30%	31.34%	18.79%	NA
All Indica	2759	9.00%	12.00%	49.51%	29.47%	NA
All Japonica	1512	97.60%	0.00%	0.53%	1.85%	NA
Aus	269	35.30%	19.30%	32.34%	13.01%	NA
Indica I	595	10.30%	10.30%	40.34%	39.16%	NA
Indica II	465	11.60%	2.20%	58.49%	27.74%	NA
Indica III	913	3.70%	18.00%	53.34%	24.97%	NA
Indica Intermediate	786	12.70%	12.20%	46.69%	28.37%	NA
Temperate Japonica	767	99.10%	0.00%	0.26%	0.65%	NA
Tropical Japonica	504	95.20%	0.00%	0.99%	3.77%	NA
Japonica Intermediate	241	97.90%	0.00%	0.41%	1.66%	NA
VI/Aromatic	96	93.80%	1.00%	5.21%	0.00%	NA
Intermediate	90	63.30%	6.70%	16.67%	13.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0116963933	T -> A	LOC_Os01g31020.1	missense_variant ; p.Asn501Lys; MODERATE	nonsynonymous_codon	Average:18.857; most accessible tissue: Callus, score: 66.968	unknown	unknown	TOLERATED	0.22
vg0116963933	T -> A	LOC_Os01g31020.1	missense_variant ; p.Asn501Lys; MODERATE	nonsynonymous_codon	Average:18.857; most accessible tissue: Callus, score: 66.968	unknown	unknown	TOLERATED	1.00
vg0116963933	T -> DEL	LOC_Os01g31020.1	N	frameshift_variant	Average:18.857; most accessible tissue: Callus, score: 66.968	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0116963933	8.68E-06	NA	mr1707_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
vg0116963933	6.96E-07	NA	mr1707_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
vg0116963933	NA	2.24E-23	mr1708_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