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Detailed information for vg0122125670:

Variant ID: vg0122125670 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 22125670
Reference Allele: A	Alternative Allele: C
Primary Allele: C	Secondary Allele: A

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, A: 0.00, others allele: 0.00, population size: 259. )

Flanking Sequence (100 bp) in Reference Genome:

CCATGTTATTAGTGCATTTATTTACTGATATTATTATCTTGATTTGTTCTTATACCAATGTTTCCTTGCCTTTTAGCTTGTCAACCCTGCATACCAAAAT[A/C]
TTTTGGATCATTTACGGACTAGAACTTTAGAAGTATTTAAGGAGTCCTTTGACAAGTCCCTAGAAAAGGAGGGTTTTGCTGTTGCTGCTCGTGACTGTAC

Reverse complement sequence

GTACAGTCACGAGCAGCAACAGCAAAACCCTCCTTTTCTAGGGACTTGTCAAAGGACTCCTTAAATACTTCTAAAGTTCTAGTCCGTAAATGATCCAAAA[T/G]
ATTTTGGTATGCAGGGTTGACAAGCTAAAAGGCAAGGAAACATTGGTATAAGAACAAATCAAGATAATAATATCAGTAAATAAATGCACTAATAACATGG

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	55.20%	44.70%	0.08%	0.00%	NA
All Indica	2759	85.80%	14.10%	0.07%	0.00%	NA
All Japonica	1512	0.50%	99.50%	0.00%	0.00%	NA
Aus	269	71.70%	27.90%	0.37%	0.00%	NA
Indica I	595	99.30%	0.70%	0.00%	0.00%	NA
Indica II	465	93.10%	6.70%	0.22%	0.00%	NA
Indica III	913	75.50%	24.50%	0.00%	0.00%	NA
Indica Intermediate	786	83.20%	16.70%	0.13%	0.00%	NA
Temperate Japonica	767	0.10%	99.90%	0.00%	0.00%	NA
Tropical Japonica	504	0.60%	99.40%	0.00%	0.00%	NA
Japonica Intermediate	241	1.20%	98.80%	0.00%	0.00%	NA
VI/Aromatic	96	10.40%	89.60%	0.00%	0.00%	NA
Intermediate	90	37.80%	61.10%	1.11%	0.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0122125670	A -> C	LOC_Os01g39310.1	missense_variant ; p.Ile370Leu; MODERATE	nonsynonymous_codon ; I370L	Average:54.484; most accessible tissue: Zhenshan97 root, score: 66.982	benign	-1.22	TOLERATED	0.38
vg0122125670	A -> C	LOC_Os01g39310.3	missense_variant ; p.Ile370Leu; MODERATE	nonsynonymous_codon ; I370L	Average:54.484; most accessible tissue: Zhenshan97 root, score: 66.982	benign	-1.22	TOLERATED	0.43

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0122125670	NA	2.89E-21	mr1003	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
vg0122125670	NA	2.11E-15	mr1156	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
vg0122125670	NA	2.94E-06	mr1156	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
vg0122125670	NA	2.35E-17	mr1566	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
vg0122125670	NA	4.30E-20	mr1580	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
vg0122125670	NA	1.18E-42	mr1591	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
vg0122125670	NA	1.33E-26	mr1051_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
vg0122125670	NA	7.80E-13	mr1191_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
vg0122125670	NA	2.06E-23	mr1609_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
vg0122125670	NA	7.56E-07	mr1619_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
vg0122125670	6.58E-06	6.59E-06	mr1747_2	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
vg0122125670	NA	2.32E-06	mr1795_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
vg0122125670	NA	6.81E-06	mr1888_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