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Detailed information for vg0513901793:

Variant ID: vg0513901793 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 13901793
Reference Allele: G	Alternative Allele: A,T
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AGCACAAGATGAAGTTGAATCTAATCTCTCTGCATCCAAGTATTTGGAAAGTTGTTTGTACAGGTGTTGATGTACCCCATGATGATATGGAGCTCACTTC[G/A,T]
GAGCAAGAGCAACTCATCCACCGCAATGCTCAAGCTTCCAATGCAATTCTCTCCGCCTTGAGTCCGGAGGAGTTCAACAAGGTTGATGGGTCTGAGGAGG

Reverse complement sequence

CCTCCTCAGACCCATCAACCTTGTTGAACTCCTCCGGACTCAAGGCGGAGAGAATTGCATTGGAAGCTTGAGCATTGCGGTGGATGAGTTGCTCTTGCTC[C/T,A]
GAAGTGAGCTCCATATCATCATGGGGTACATCAACACCTGTACAAACAACTTTCCAAATACTTGGATGCAGAGAGATTAGATTCAACTTCATCTTGTGCT

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	86.70%	0.20%	1.23%	11.81%	T: 0.11%
All Indica	2759	80.40%	0.30%	1.99%	17.22%	T: 0.18%
All Japonica	1512	95.80%	0.10%	0.13%	3.97%	NA
Aus	269	98.50%	0.00%	0.37%	1.12%	NA
Indica I	595	80.30%	0.70%	3.19%	15.80%	NA
Indica II	465	68.80%	0.00%	2.37%	28.60%	T: 0.22%
Indica III	913	88.20%	0.10%	0.77%	10.62%	T: 0.33%
Indica Intermediate	786	78.10%	0.30%	2.29%	19.21%	T: 0.13%
Temperate Japonica	767	97.80%	0.00%	0.26%	1.96%	NA
Tropical Japonica	504	94.00%	0.20%	0.00%	5.75%	NA
Japonica Intermediate	241	93.40%	0.00%	0.00%	6.64%	NA
VI/Aromatic	96	90.60%	0.00%	0.00%	9.38%	NA
Intermediate	90	87.80%	0.00%	0.00%	12.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0513901793	G -> T	LOC_Os05g24100.1	synonymous_variant ; p.Ser97Ser; LOW	synonymous_codon	Average:20.069; most accessible tissue: Zhenshan97 panicle, score: 36.038	N	N	N	N
vg0513901793	G -> DEL	LOC_Os05g24100.1	N	frameshift_variant	Average:20.069; most accessible tissue: Zhenshan97 panicle, score: 36.038	N	N	N	N
vg0513901793	G -> A	LOC_Os05g24100.1	synonymous_variant ; p.Ser97Ser; LOW	synonymous_codon	Average:20.069; most accessible tissue: Zhenshan97 panicle, score: 36.038	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0513901793	7.12E-06	NA	mr1013	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
vg0513901793	8.93E-06	NA	mr1218_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