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Detailed information for vg0113027104:

Variant ID: vg0113027104 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 13027104
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 108. )

Flanking Sequence (100 bp) in Reference Genome:

TAGCGTTTGAGAAGATTTTGTACATTCTCTCCTTCATGACCTTAAAATCAAGAGAGTCTGGATCTTCACGGTTCGGGTCATGCTTGCCATCAAACTCAAA[G/A]
GCCGTACGGGATCTCTCTTTAATTGGAGCTAGCCGGCTCTTGATAAAATGCCGGGTGATCTGTTCTCCTTGCAGGCCTTGCTCCTTCAGTTTCAGCATAC

Reverse complement sequence

GTATGCTGAAACTGAAGGAGCAAGGCCTGCAAGGAGAACAGATCACCCGGCATTTTATCAAGAGCCGGCTAGCTCCAATTAAAGAGAGATCCCGTACGGC[C/T]
TTTGAGTTTGATGGCAAGCATGACCCGAACCGTGAAGATCCAGACTCTCTTGATTTTAAGGTCATGAAGGAGAGAATGTACAAAATCTTCTCAAACGCTA

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	61.80%	4.70%	2.90%	30.60%	NA
All Indica	2759	42.30%	7.60%	4.20%	45.89%	NA
All Japonica	1512	96.20%	0.30%	0.40%	3.11%	NA
Aus	269	50.60%	1.10%	4.09%	44.24%	NA
Indica I	595	57.80%	1.20%	2.18%	38.82%	NA
Indica II	465	44.70%	3.70%	7.10%	44.52%	NA
Indica III	913	27.20%	15.20%	3.72%	53.89%	NA
Indica Intermediate	786	46.80%	5.90%	4.58%	42.75%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	89.70%	0.40%	1.19%	8.73%	NA
Japonica Intermediate	241	97.90%	0.80%	0.00%	1.24%	NA
VI/Aromatic	96	89.60%	2.10%	2.08%	6.25%	NA
Intermediate	90	84.40%	4.40%	2.22%	8.89%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0113027104	G -> A	LOC_Os01g23180.1	synonymous_variant ; p.Ala120Ala; LOW	synonymous_codon	Average:11.34; most accessible tissue: Callus, score: 28.764	N	N	N	N
vg0113027104	G -> DEL	LOC_Os01g23180.1	N	frameshift_variant	Average:11.34; most accessible tissue: Callus, score: 28.764	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0113027104	5.42E-07	7.58E-10	mr1238	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
vg0113027104	5.02E-06	5.15E-08	mr1309	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
vg0113027104	2.87E-07	5.64E-11	mr1841	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
vg0113027104	5.44E-08	5.44E-08	mr1900	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
vg0113027104	1.42E-06	4.12E-09	mr1238_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
vg0113027104	3.07E-06	3.49E-08	mr1484_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
vg0113027104	1.34E-06	5.10E-11	mr1841_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
vg0113027104	NA	5.37E-08	mr1900_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