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Detailed information for vg0225367493:

Variant ID: vg0225367493 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 25367493
Reference Allele: G	Alternative Allele: T
Primary Allele: G	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GTCAAGGGTGCGTATAACTCTACTTCCCCTTTCCATTCAGTTCCTGAGTCGAGTGGGGGATGCCGTGGGTTTAGTTTTGGGGGTCAAATTTCTGCATCTA[G/T]
AGTAGAGTGCCCAGAGTTTGCAGGGGAAAATCCTAAGGCCTGGAAACTGAAGTGTGAGACTTATTTTGGGCTGTGTGGAACTCCTTCTGATCACTGGATT

Reverse complement sequence

AATCCAGTGATCAGAAGGAGTTCCACACAGCCCAAAATAAGTCTCACACTTCAGTTTCCAGGCCTTAGGATTTTCCCCTGCAAACTCTGGGCACTCTACT[C/A]
TAGATGCAGAAATTTGACCCCCAAAACTAAACCCACGGCATCCCCCACTCGACTCAGGAACTGAATGGAAAGGGGAAGTAGAGTTATACGCACCCTTGAC

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	59.20%	0.60%	1.52%	38.74%	NA
All Indica	2759	44.20%	0.80%	2.28%	52.74%	NA
All Japonica	1512	92.90%	0.00%	0.20%	6.94%	NA
Aus	269	10.00%	1.50%	1.12%	87.36%	NA
Indica I	595	64.70%	0.50%	0.84%	33.95%	NA
Indica II	465	43.90%	0.90%	1.94%	53.33%	NA
Indica III	913	36.40%	0.70%	2.74%	60.24%	NA
Indica Intermediate	786	38.00%	1.00%	3.05%	57.89%	NA
Temperate Japonica	767	98.60%	0.00%	0.13%	1.30%	NA
Tropical Japonica	504	87.10%	0.00%	0.40%	12.50%	NA
Japonica Intermediate	241	86.70%	0.00%	0.00%	13.28%	NA
VI/Aromatic	96	88.50%	0.00%	1.04%	10.42%	NA
Intermediate	90	67.80%	1.10%	2.22%	28.89%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0225367493	G -> T	LOC_Os02g42180.1	missense_variant ; p.Arg185Ile; MODERATE	nonsynonymous_codon ; R185I	Average:66.414; most accessible tissue: Minghui63 flag leaf, score: 73.334	unknown	unknown	DELETERIOUS	0.04
vg0225367493	G -> DEL	LOC_Os02g42180.1	N	frameshift_variant	Average:66.414; most accessible tissue: Minghui63 flag leaf, score: 73.334	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0225367493	NA	6.78E-07	mr1077	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
vg0225367493	2.97E-06	1.30E-07	mr1509	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
vg0225367493	NA	1.96E-06	mr1558_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