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Detailed information for vg0412575333:

Variant ID: vg0412575333 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 12575333
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: 50. )

Flanking Sequence (100 bp) in Reference Genome:

TACCACAACCATGAGTACACACCGATCTATCAAAGAATAAAGTCCACGGCACTATATCAACTGAGCCAATTGAATCATTATGATGTTCCACAATAAAATC[G/A]
GCCATAGCTTGTCCCTTAATTGCCTTCAACGACTCATACCGAAGATCAAACTCGGTTAAGGAAAATATCCACTTTTCAACCCTTCCTTTCAATATTGGAG

Reverse complement sequence

CTCCAATATTGAAAGGAAGGGTTGAAAAGTGGATATTTTCCTTAACCGAGTTTGATCTTCGGTATGAGTCGTTGAAGGCAATTAAGGGACAAGCTATGGC[C/T]
GATTTTATTGTGGAACATCATAATGATTCAATTGGCTCAGTTGATATAGTGCCGTGGACTTTATTCTTTGATAGATCGGTGTGTACTCATGGTTGTGGTA

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	29.20%	11.90%	1.27%	57.62%	NA
All Indica	2759	8.80%	0.50%	0.80%	89.82%	NA
All Japonica	1512	57.80%	34.80%	2.05%	5.36%	NA
Aus	269	51.70%	0.40%	0.74%	47.21%	NA
Indica I	595	0.70%	0.20%	1.18%	97.98%	NA
Indica II	465	18.90%	1.30%	1.08%	78.71%	NA
Indica III	913	9.50%	0.30%	0.22%	89.92%	NA
Indica Intermediate	786	8.30%	0.60%	1.02%	90.08%	NA
Temperate Japonica	767	91.10%	3.30%	2.09%	3.52%	NA
Tropical Japonica	504	12.70%	84.30%	1.98%	0.99%	NA
Japonica Intermediate	241	46.10%	31.50%	2.07%	20.33%	NA
VI/Aromatic	96	92.70%	5.20%	0.00%	2.08%	NA
Intermediate	90	38.90%	16.70%	5.56%	38.89%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0412575333	G -> DEL	LOC_Os04g22200.1	N	frameshift_variant	Average:8.453; most accessible tissue: Callus, score: 27.862	N	N	N	N
vg0412575333	G -> A	LOC_Os04g22200.1	synonymous_variant ; p.Ala1084Ala; LOW	synonymous_codon	Average:8.453; most accessible tissue: Callus, score: 27.862	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0412575333	1.26E-07	NA	mr1071	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
vg0412575333	7.13E-08	NA	mr1140	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
vg0412575333	5.55E-06	NA	mr1203	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
vg0412575333	NA	1.71E-22	mr1301	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
vg0412575333	4.49E-06	NA	mr1395	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
vg0412575333	NA	1.53E-18	mr1552	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
vg0412575333	NA	3.19E-10	mr1552	Jap_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
vg0412575333	NA	3.15E-07	mr1554	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
vg0412575333	NA	7.25E-10	mr1580	Jap_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
vg0412575333	5.70E-08	NA	mr1618	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
vg0412575333	NA	8.50E-09	mr1648	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
vg0412575333	2.35E-06	NA	mr1757	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
vg0412575333	NA	1.49E-12	mr1905	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
vg0412575333	NA	1.45E-07	mr1993	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
vg0412575333	NA	3.65E-09	mr1993	Jap_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
vg0412575333	NA	5.13E-12	mr1097_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
vg0412575333	4.07E-06	NA	mr1203_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
vg0412575333	NA	1.55E-19	mr1301_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
vg0412575333	NA	1.14E-06	mr1363_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
vg0412575333	2.21E-06	NA	mr1549_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
vg0412575333	NA	1.86E-12	mr1553_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
vg0412575333	NA	3.81E-10	mr1580_2	Jap_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
vg0412575333	NA	2.91E-29	mr1699_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
vg0412575333	NA	1.97E-07	mr1786_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