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Detailed information for vg1218152575:

Variant ID: vg1218152575 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 18152575
Reference Allele: A	Alternative Allele: C
Primary Allele: C	Secondary Allele: A

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.88, C: 0.12, others allele: 0.00, population size: 92. )

Flanking Sequence (100 bp) in Reference Genome:

CACAACCCCGTCTGGCACCTGCGCCTTCCTGAAGCTACGACAGAACTCCGCCCAAGTGACTTCTGTGCCTGGCGGGTGGGTAGCCATGTGATTGTCCCAC[A/C]
AAGCTGACGCGGGACCCTGGAGCTGGTGTGTGGCAAAGGCGACCTTGTCCTGATCATTGCACTGCATAAGGTTTAGCTTCTTCTCTATGGCATGGAGCCA

Reverse complement sequence

TGGCTCCATGCCATAGAGAAGAAGCTAAACCTTATGCAGTGCAATGATCAGGACAAGGTCGCCTTTGCCACACACCAGCTCCAGGGTCCCGCGTCAGCTT[T/G]
GTGGGACAATCACATGGCTACCCACCCGCCAGGCACAGAAGTCACTTGGGCGGAGTTCTGTCGTAGCTTCAGGAAGGCGCAGGTGCCAGACGGGGTTGTG

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	61.20%	36.40%	1.71%	0.63%	NA
All Indica	2759	93.70%	5.10%	1.01%	0.14%	NA
All Japonica	1512	9.10%	89.20%	0.73%	0.93%	NA
Aus	269	49.10%	35.30%	13.38%	2.23%	NA
Indica I	595	93.40%	6.10%	0.50%	0.00%	NA
Indica II	465	95.90%	3.40%	0.65%	0.00%	NA
Indica III	913	96.30%	2.50%	0.99%	0.22%	NA
Indica Intermediate	786	89.60%	8.50%	1.65%	0.25%	NA
Temperate Japonica	767	1.30%	98.20%	0.26%	0.26%	NA
Tropical Japonica	504	20.60%	75.60%	1.59%	2.18%	NA
Japonica Intermediate	241	10.00%	89.20%	0.41%	0.41%	NA
VI/Aromatic	96	13.50%	81.20%	2.08%	3.12%	NA
Intermediate	90	27.80%	64.40%	4.44%	3.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1218152575	A -> C	LOC_Os12g30250.1	missense_variant ; p.Leu39Trp; MODERATE	nonsynonymous_codon ; L39W	Average:30.631; most accessible tissue: Callus, score: 44.227	possibly damaging	-1.781	TOLERATED	1.00
vg1218152575	A -> DEL	LOC_Os12g30250.1	N	frameshift_variant	Average:30.631; most accessible tissue: Callus, score: 44.227	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1218152575	7.69E-06	NA	mr1016	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
vg1218152575	1.56E-07	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
vg1218152575	3.03E-07	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
vg1218152575	4.50E-06	NA	mr1023	Jap_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
vg1218152575	NA	2.18E-11	mr1084	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
vg1218152575	5.85E-06	NA	mr1132	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
vg1218152575	3.23E-07	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
vg1218152575	NA	8.58E-13	mr1239	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
vg1218152575	NA	7.69E-17	mr1376	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
vg1218152575	NA	7.69E-17	mr1431	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
vg1218152575	9.25E-06	NA	mr1490	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
vg1218152575	NA	3.27E-06	mr1646	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
vg1218152575	NA	6.36E-11	mr1775	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