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Detailed information for vg0301371740:

Variant ID: vg0301371740 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 1371740
Reference Allele: A	Alternative Allele: C
Primary Allele: A	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 93. )

Flanking Sequence (100 bp) in Reference Genome:

GCAAATACCACGATTTCATGCGTATCAGGGGTCGGGAATGCTTCGCCGAATGCCGGTCGCCACCCGATGATCTCCTTTGCTAGAAGAACGCCGTGCGCCA[A/C]
CATCTCCTTCAGATTATCTTCCGTCACATCAGAGGGCGCCCACTGACTCTCGAAGCTTTCTCTTTTTTCCGCCATGAATGTGGACTGGATGGTTTGATTT

Reverse complement sequence

AAATCAAACCATCCAGTCCACATTCATGGCGGAAAAAAGAGAAAGCTTCGAGAGTCAGTGGGCGCCCTCTGATGTGACGGAAGATAATCTGAAGGAGATG[T/G]
TGGCGCACGGCGTTCTTCTAGCAAAGGAGATCATCGGGTGGCGACCGGCATTCGGCGAAGCATTCCCGACCCCTGATACGCATGAAATCGTGGTATTTGC

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	30.70%	19.30%	1.84%	48.18%	NA
All Indica	2759	3.20%	14.40%	2.75%	79.63%	NA
All Japonica	1512	84.30%	15.40%	0.00%	0.26%	NA
Aus	269	18.60%	73.60%	1.86%	5.95%	NA
Indica I	595	4.00%	9.90%	2.02%	84.03%	NA
Indica II	465	7.10%	10.30%	3.44%	79.14%	NA
Indica III	913	0.80%	18.50%	1.97%	78.75%	NA
Indica Intermediate	786	3.20%	15.40%	3.82%	77.61%	NA
Temperate Japonica	767	94.70%	5.20%	0.00%	0.13%	NA
Tropical Japonica	504	69.60%	30.00%	0.00%	0.40%	NA
Japonica Intermediate	241	82.20%	17.40%	0.00%	0.41%	NA
VI/Aromatic	96	8.30%	60.40%	0.00%	31.25%	NA
Intermediate	90	31.10%	28.90%	6.67%	33.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0301371740	A -> C	LOC_Os03g03220.1	missense_variant ; p.Leu26Val; MODERATE	nonsynonymous_codon ; L26V	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	benign	-0.139	TOLERATED	1.00
vg0301371740	A -> DEL	LOC_Os03g03220.1	N	frameshift_variant	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0301371740	NA	6.15E-06	mr1048	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
vg0301371740	NA	2.93E-07	mr1190	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
vg0301371740	NA	3.33E-06	mr1262	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
vg0301371740	NA	8.18E-07	mr1286	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
vg0301371740	NA	8.17E-06	mr1331	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
vg0301371740	NA	7.15E-06	mr1445	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
vg0301371740	NA	9.83E-06	mr1485	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
vg0301371740	NA	2.61E-06	mr1574	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
vg0301371740	NA	2.52E-06	mr1665	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
vg0301371740	NA	3.44E-06	mr1759	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
vg0301371740	NA	9.91E-06	mr1774	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
vg0301371740	NA	6.32E-07	mr1777	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
vg0301371740	1.69E-06	2.77E-08	mr1979	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