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Detailed information for vg0224605253:

Variant ID: vg0224605253 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 24605253
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CTTGTGCTGGAATGAGGTGGGCGAAGCACTGGTATTCGGTCCTGACGTACTCAAGGCAGCAGAAGAACAAGTTAAACTGATCCGAGAACGTTTAAAGACA[G/A]
CGCAGAACCGTCAGAAGAATTACGCGGACAATCGAAGGCGTGACCTTGAGTTCGAAAAAGGAGATCATGTGTACCTGCGGGTATCGCCTCTCCGTGGTAT

Reverse complement sequence

ATACCACGGAGAGGCGATACCCGCAGGTACACATGATCTCCTTTTTCGAACTCAAGGTCACGCCTTCGATTGTCCGCGTAATTCTTCTGACGGTTCTGCG[C/T]
TGTCTTTAAACGTTCTCGGATCAGTTTAACTTGTTCTTCTGCTGCCTTGAGTACGTCAGGACCGAATACCAGTGCTTCGCCCACCTCATTCCAGCACAAG

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	82.10%	3.30%	1.18%	13.42%	NA
All Indica	2759	81.00%	5.40%	1.27%	12.32%	NA
All Japonica	1512	79.50%	0.20%	1.39%	18.92%	NA
Aus	269	99.30%	0.00%	0.00%	0.74%	NA
Indica I	595	45.20%	18.00%	2.02%	34.79%	NA
Indica II	465	84.30%	6.00%	2.80%	6.88%	NA
Indica III	913	98.10%	0.00%	0.00%	1.86%	NA
Indica Intermediate	786	86.30%	1.80%	1.27%	10.69%	NA
Temperate Japonica	767	70.40%	0.40%	1.43%	27.77%	NA
Tropical Japonica	504	94.00%	0.00%	1.19%	4.76%	NA
Japonica Intermediate	241	78.00%	0.00%	1.66%	20.33%	NA
VI/Aromatic	96	97.90%	0.00%	0.00%	2.08%	NA
Intermediate	90	93.30%	2.20%	0.00%	4.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0224605253	G -> A	LOC_Os02g40570.1	missense_variant ; p.Ala1660Thr; MODERATE	nonsynonymous_codon ; A1660T	Average:17.291; most accessible tissue: Minghui63 panicle, score: 38.588	benign	0.573	DELETERIOUS	0.02
vg0224605253	G -> DEL	LOC_Os02g40570.1	N	frameshift_variant	Average:17.291; most accessible tissue: Minghui63 panicle, score: 38.588	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0224605253	5.85E-13	4.20E-16	mr1191	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
vg0224605253	2.17E-12	1.32E-12	mr1191	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
vg0224605253	1.10E-12	1.26E-15	mr1644	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
vg0224605253	1.67E-11	2.61E-12	mr1644	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
vg0224605253	NA	9.45E-08	mr1662	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
vg0224605253	NA	6.84E-08	mr1662	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
vg0224605253	6.94E-14	1.13E-22	mr1191_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
vg0224605253	2.00E-12	2.81E-17	mr1191_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
vg0224605253	NA	9.96E-06	mr1566_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
vg0224605253	NA	1.38E-06	mr1662_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
vg0224605253	NA	5.12E-06	mr1662_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
vg0224605253	4.41E-06	NA	mr1897_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