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Detailed information for vg0414059272:

Variant ID: vg0414059272 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 14059272
Reference Allele: C	Alternative Allele: A
Primary Allele: C	Secondary Allele: A

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.83, A: 0.18, others allele: 0.00, population size: 90. )

Flanking Sequence (100 bp) in Reference Genome:

TTGGTTATAGGTGCAAGTGCAAGCATGGCTTTGAAGGGAATCCGTCTATCAAAGATGGTTGCCAAGGTTTGTCTCTGTCCCTTTTCACAAGCACAGTTAG[C/A]
ATTGCTTCACAATTTAACGCACTTGGACACAGCCAACATATATATTGGTACTCTCTCCGTCGCATAAAAATTACATTTCTAGCTAATTTAGGACAAATCA

Reverse complement sequence

TGATTTGTCCTAAATTAGCTAGAAATGTAATTTTTATGCGACGGAGAGAGTACCAATATATATGTTGGCTGTGTCCAAGTGCGTTAAATTGTGAAGCAAT[G/T]
CTAACTGTGCTTGTGAAAAGGGACAGAGACAAACCTTGGCAACCATCTTTGATAGACGGATTCCCTTCAAAGCCATGCTTGCACTTGCACCTATAACCAA

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	55.90%	43.90%	0.15%	0.02%	NA
All Indica	2759	44.00%	55.70%	0.18%	0.04%	NA
All Japonica	1512	86.60%	13.40%	0.00%	0.00%	NA
Aus	269	13.00%	87.00%	0.00%	0.00%	NA
Indica I	595	71.60%	28.20%	0.17%	0.00%	NA
Indica II	465	15.90%	83.90%	0.22%	0.00%	NA
Indica III	913	40.20%	59.80%	0.00%	0.00%	NA
Indica Intermediate	786	44.30%	55.20%	0.38%	0.13%	NA
Temperate Japonica	767	96.60%	3.40%	0.00%	0.00%	NA
Tropical Japonica	504	83.10%	16.90%	0.00%	0.00%	NA
Japonica Intermediate	241	62.20%	37.80%	0.00%	0.00%	NA
VI/Aromatic	96	40.60%	59.40%	0.00%	0.00%	NA
Intermediate	90	50.00%	47.80%	2.22%	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
vg0414059272	C -> DEL	N	N	silent_mutation	Average:58.027; most accessible tissue: Callus, score: 77.469	N	N	N	N
vg0414059272	C -> A	LOC_Os04g24510.1	intron_variant ; MODIFIER	silent_mutation	Average:58.027; most accessible tissue: Callus, score: 77.469	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0414059272	NA	5.30E-06	mr1114_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
vg0414059272	NA	3.80E-07	mr1350_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
vg0414059272	9.01E-06	NA	mr1584_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
vg0414059272	3.52E-08	NA	mr1730_2	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
vg0414059272	4.76E-06	2.42E-07	mr1730_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
vg0414059272	NA	1.39E-14	mr1846_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
vg0414059272	NA	4.89E-08	mr1846_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
vg0414059272	3.17E-06	NA	mr1866_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