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Detailed information for vg0417840360:

Variant ID: vg0417840360 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 17840360
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 291. )

Flanking Sequence (100 bp) in Reference Genome:

GCTGGTCCGAGTCCGACCCTGTTTCGTCGGGTCTCGAGGTTTCCTTGCTCGGGAAGGCATGTTTTGGGTTTCCTTTGGTTTCTACCCCGAGTTGGACGTG[G/A]
AGGAGGGCCTGTAGAGGGCAAGACCAACCCCTGTATAAGGGACAAGGCCGGTTCATTGTAAAATCAATCTACTATCAATCAATCGAATCGTTCTTTTCAT

Reverse complement sequence

ATGAAAAGAACGATTCGATTGATTGATAGTAGATTGATTTTACAATGAACCGGCCTTGTCCCTTATACAGGGGTTGGTCTTGCCCTCTACAGGCCCTCCT[C/T]
CACGTCCAACTCGGGGTAGAAACCAAAGGAAACCCAAAACATGCCTTCCCGAGCAAGGAAACCTCGAGACCCGACGAAACAGGGTCGGACTCGGACCAGC

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	35.70%	12.80%	1.76%	49.75%	NA
All Indica	2759	41.80%	1.30%	2.32%	54.62%	NA
All Japonica	1512	16.30%	34.50%	0.86%	48.35%	NA
Aus	269	69.50%	0.00%	0.74%	29.74%	NA
Indica I	595	73.80%	0.30%	1.01%	24.87%	NA
Indica II	465	24.30%	4.50%	4.52%	66.67%	NA
Indica III	913	27.30%	0.20%	1.31%	71.19%	NA
Indica Intermediate	786	44.70%	1.40%	3.18%	50.76%	NA
Temperate Japonica	767	14.30%	3.30%	1.43%	80.96%	NA
Tropical Japonica	504	22.20%	68.80%	0.00%	8.93%	NA
Japonica Intermediate	241	10.00%	62.20%	0.83%	26.97%	NA
VI/Aromatic	96	63.50%	30.20%	1.04%	5.21%	NA
Intermediate	90	44.40%	21.10%	3.33%	31.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0417840360	G -> DEL	N	N	silent_mutation	Average:20.37; most accessible tissue: Minghui63 panicle, score: 34.226	N	N	N	N
vg0417840360	G -> A	LOC_Os04g29920.1	downstream_gene_variant ; 458.0bp to feature; MODIFIER	silent_mutation	Average:20.37; most accessible tissue: Minghui63 panicle, score: 34.226	N	N	N	N
vg0417840360	G -> A	LOC_Os04g29920-LOC_Os04g29930	intergenic_region ; MODIFIER	silent_mutation	Average:20.37; most accessible tissue: Minghui63 panicle, score: 34.226	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0417840360	NA	3.95E-08	mr1156_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
vg0417840360	NA	8.00E-06	mr1278_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
vg0417840360	NA	2.00E-06	mr1369_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
vg0417840360	NA	8.69E-06	mr1397_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
vg0417840360	NA	3.36E-06	mr1467_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
vg0417840360	3.20E-06	NA	mr1663_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
vg0417840360	NA	6.53E-06	mr1665_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
vg0417840360	NA	2.16E-06	mr1812_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
vg0417840360	NA	5.42E-06	mr1832_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
vg0417840360	NA	4.21E-12	mr1851_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
vg0417840360	NA	3.19E-16	mr1864_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
vg0417840360	6.32E-06	6.31E-06	mr1983_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