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Detailed information for vg1017360881:

Variant ID: vg1017360881 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 17360881
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.96, A: 0.04, others allele: 0.00, population size: 49. )

Flanking Sequence (100 bp) in Reference Genome:

CGGTGAGATTGTTGCCGGCCATCCGCAGGTCCTGCAGCTTCATCAACTTCCCGAGCGACGCCGGAATCGAGCCGGAGAACGCATTGATGGACAGGTTGAG[G/A]
TACCTCAGATTCGGGAGCTTCTCCGGCAGCGTGTCCGGTATCTTCCCGAACAGAGTATTCTGCGACAGGTCGAGGTAGGTGATGTTGCCGCTCCTGAGGA

Reverse complement sequence

TCCTCAGGAGCGGCAACATCACCTACCTCGACCTGTCGCAGAATACTCTGTTCGGGAAGATACCGGACACGCTGCCGGAGAAGCTCCCGAATCTGAGGTA[C/T]
CTCAACCTGTCCATCAATGCGTTCTCCGGCTCGATTCCGGCGTCGCTCGGGAAGTTGATGAAGCTGCAGGACCTGCGGATGGCCGGCAACAATCTCACCG

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	54.00%	2.80%	2.22%	40.99%	NA
All Indica	2759	32.10%	4.40%	2.90%	60.60%	NA
All Japonica	1512	91.00%	0.40%	0.79%	7.80%	NA
Aus	269	59.50%	0.00%	3.72%	36.80%	NA
Indica I	595	9.20%	9.10%	7.06%	74.62%	NA
Indica II	465	26.00%	3.70%	2.37%	67.96%	NA
Indica III	913	47.40%	3.20%	1.53%	47.86%	NA
Indica Intermediate	786	35.10%	2.80%	1.65%	60.43%	NA
Temperate Japonica	767	98.20%	0.30%	0.13%	1.43%	NA
Tropical Japonica	504	91.30%	0.80%	1.59%	6.35%	NA
Japonica Intermediate	241	67.60%	0.00%	1.24%	31.12%	NA
VI/Aromatic	96	75.00%	0.00%	1.04%	23.96%	NA
Intermediate	90	67.80%	2.20%	2.22%	27.78%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1017360881	G -> A	LOC_Os10g33130.1	synonymous_variant ; p.Tyr247Tyr; LOW	synonymous_codon	Average:36.382; most accessible tissue: Zhenshan97 flag leaf, score: 80.373	N	N	N	N
vg1017360881	G -> DEL	LOC_Os10g33130.1	N	frameshift_variant	Average:36.382; most accessible tissue: Zhenshan97 flag leaf, score: 80.373	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1017360881	2.87E-06	2.21E-10	mr1038	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
vg1017360881	NA	8.59E-09	mr1038	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
vg1017360881	5.57E-07	1.84E-06	mr1344	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
vg1017360881	NA	5.00E-06	mr1344	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
vg1017360881	5.24E-06	1.01E-11	mr1389	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
vg1017360881	NA	8.53E-09	mr1389	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
vg1017360881	NA	5.25E-06	mr1518	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
vg1017360881	NA	2.88E-06	mr1534	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
vg1017360881	NA	5.78E-06	mr1571	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
vg1017360881	5.85E-06	1.09E-07	mr1716	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
vg1017360881	NA	1.24E-06	mr1745	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
vg1017360881	NA	1.56E-06	mr1798	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
vg1017360881	NA	3.02E-06	mr1974	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
vg1017360881	NA	2.47E-08	mr1038_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
vg1017360881	NA	6.33E-07	mr1389_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