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Detailed information for vg0401349008:

Variant ID: vg0401349008 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 1349008
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.88, G: 0.10, others allele: 0.00, population size: 49. )

Flanking Sequence (100 bp) in Reference Genome:

CGTATCTTAGAGACAGATGAGAGAAGAACTAGGAATCGAGTTATCCGTTTCTGCAAGGTCCAATGGAGTAATCACTCGGAAGAAGAAGCTACCTGGGAGC[A/G]
AGAAGATGAATTAAAGTCAGCTCATCCGCATCTTTTCGCCAGCTCTTCCGAATCTCGAGGACGAGATTCTGTTTAATGGGGATAGGTTTGTCACACCCTA

Reverse complement sequence

TAGGGTGTGACAAACCTATCCCCATTAAACAGAATCTCGTCCTCGAGATTCGGAAGAGCTGGCGAAAAGATGCGGATGAGCTGACTTTAATTCATCTTCT[T/C]
GCTCCCAGGTAGCTTCTTCTTCCGAGTGATTACTCCATTGGACCTTGCAGAAACGGATAACTCGATTCCTAGTTCTTCTCTCATCTGTCTCTAAGATACG

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	13.10%	1.50%	5.25%	80.22%	NA
All Indica	2759	2.80%	1.60%	3.81%	91.88%	NA
All Japonica	1512	34.70%	1.20%	7.41%	56.75%	NA
Aus	269	0.70%	0.70%	4.09%	94.42%	NA
Indica I	595	1.20%	0.00%	1.01%	97.82%	NA
Indica II	465	7.70%	0.90%	5.59%	85.81%	NA
Indica III	913	1.20%	3.00%	4.38%	91.46%	NA
Indica Intermediate	786	2.80%	1.50%	4.20%	91.48%	NA
Temperate Japonica	767	49.20%	1.20%	1.96%	47.72%	NA
Tropical Japonica	504	17.10%	0.80%	13.89%	68.25%	NA
Japonica Intermediate	241	25.30%	2.10%	11.20%	61.41%	NA
VI/Aromatic	96	3.10%	3.10%	15.62%	78.12%	NA
Intermediate	90	13.30%	4.40%	5.56%	76.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0401349008	A -> DEL	LOC_Os04g03190.1	N	frameshift_variant	Average:10.725; most accessible tissue: Callus, score: 23.517	N	N	N	N
vg0401349008	A -> G	LOC_Os04g03190.1	missense_variant ; p.Gln1293Arg; MODERATE	nonsynonymous_codon ; Q1293R	Average:10.725; most accessible tissue: Callus, score: 23.517	benign	-0.909	TOLERATED	1.00

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0401349008	7.39E-08	NA	mr1016	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
vg0401349008	1.81E-06	NA	mr1017	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
vg0401349008	9.38E-07	NA	mr1018	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
vg0401349008	7.93E-06	NA	mr1023	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
vg0401349008	4.78E-08	NA	mr1055	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
vg0401349008	5.29E-08	NA	mr1132	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
vg0401349008	1.65E-06	NA	mr1142	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
vg0401349008	1.41E-06	NA	mr1390	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
vg0401349008	5.60E-07	NA	mr1489	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
vg0401349008	1.89E-06	NA	mr1490	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
vg0401349008	9.05E-06	NA	mr1778	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
vg0401349008	8.16E-06	NA	mr1805	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
vg0401349008	1.09E-07	NA	mr1019_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
vg0401349008	2.35E-08	NA	mr1055_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
vg0401349008	3.29E-08	NA	mr1132_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
vg0401349008	7.99E-06	NA	mr1178_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
vg0401349008	1.34E-06	NA	mr1390_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
vg0401349008	1.71E-06	NA	mr1489_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
vg0401349008	1.75E-06	NA	mr1490_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