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Detailed information for vg0209427613:

Variant ID: vg0209427613 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 9427613
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.97, A: 0.03, others allele: 0.00, population size: 195. )

Flanking Sequence (100 bp) in Reference Genome:

CCACCAATTAGTAGACTGATTAACTGAAAAAACAGTAGGTAAATTACCATACCCGCTTCCATCTCCAGTGTTGCCAATGGTCACATTAGCAGACTTAGAA[A/G]
TCTGCCCTGCAGGTGCCTTCATCCCCTTGCGCTGTGGACACTTCCTAGCCAGATGACCAGGTTGACCACACACAAAGCAAGTCCTCTCATCCTGATTAGG

Reverse complement sequence

CCTAATCAGGATGAGAGGACTTGCTTTGTGTGTGGTCAACCTGGTCATCTGGCTAGGAAGTGTCCACAGCGCAAGGGGATGAAGGCACCTGCAGGGCAGA[T/C]
TTCTAAGTCTGCTAATGTGACCATTGGCAACACTGGAGATGGAAGCGGGTATGGTAATTTACCTACTGTTTTTTCAGTTAATCAGTCTACTAATTGGTGG

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	37.20%	7.80%	40.99%	14.03%	NA
All Indica	2759	8.60%	8.60%	59.59%	23.20%	NA
All Japonica	1512	91.50%	5.90%	1.98%	0.60%	NA
Aus	269	3.30%	13.40%	81.04%	2.23%	NA
Indica I	595	5.70%	4.50%	58.66%	31.09%	NA
Indica II	465	4.70%	4.30%	56.13%	34.84%	NA
Indica III	913	11.10%	14.10%	62.87%	11.94%	NA
Indica Intermediate	786	10.20%	7.90%	58.52%	23.41%	NA
Temperate Japonica	767	88.10%	10.00%	1.04%	0.78%	NA
Tropical Japonica	504	96.00%	0.20%	3.57%	0.20%	NA
Japonica Intermediate	241	92.90%	4.60%	1.66%	0.83%	NA
VI/Aromatic	96	86.50%	3.10%	10.42%	0.00%	NA
Intermediate	90	51.10%	1.10%	38.89%	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
vg0209427613	A -> G	LOC_Os02g16520.1	missense_variant ; p.Ile237Thr; MODERATE	nonsynonymous_codon ; I237T	Average:24.379; most accessible tissue: Minghui63 panicle, score: 34.226	possibly damaging	-1.851	TOLERATED	1.00
vg0209427613	A -> DEL	LOC_Os02g16520.1	N	frameshift_variant	Average:24.379; most accessible tissue: Minghui63 panicle, score: 34.226	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0209427613	NA	1.75E-07	mr1063	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
vg0209427613	NA	5.58E-06	mr1069	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
vg0209427613	NA	6.03E-06	mr1170	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
vg0209427613	NA	9.79E-08	mr1177	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
vg0209427613	NA	2.54E-09	mr1180	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
vg0209427613	NA	8.11E-09	mr1183	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
vg0209427613	NA	1.17E-06	mr1195	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
vg0209427613	NA	2.81E-07	mr1220	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
vg0209427613	NA	1.27E-07	mr1352	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
vg0209427613	5.47E-06	7.07E-08	mr1441	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
vg0209427613	NA	1.06E-08	mr1503	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
vg0209427613	NA	6.12E-06	mr1743	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
vg0209427613	NA	5.25E-06	mr1785	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