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Detailed information for vg0502283394:

Variant ID: vg0502283394 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 2283394
Reference Allele: C	Alternative Allele: A
Primary Allele: C	Secondary Allele: A

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.95, A: 0.07, others allele: 0.00, population size: 59. )

Flanking Sequence (100 bp) in Reference Genome:

CACTGACCAAGACCAAACCCGTCAAAGGTGAGGGTTTGGGCCCGTCAGAGATGACCTGGTCCGGCGTAGTTAAATACTTTCTCCGTTTCATAATGTAAGT[C/A]
TTTCTAGTATTGTCCATATTCATATAGATGTTAATGAATCTAGATACATTCATATAAATGTTAATGAATATAAATATAACATATATATTTATATTCATTA

Reverse complement sequence

TAATGAATATAAATATATATGTTATATTTATATTCATTAACATTTATATGAATGTATCTAGATTCATTAACATCTATATGAATATGGACAATACTAGAAA[G/T]
ACTTACATTATGAAACGGAGAAAGTATTTAACTACGCCGGACCAGGTCATCTCTGACGGGCCCAAACCCTCACCTTTGACGGGTTTGGTCTTGGTCAGTG

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	45.40%	2.10%	8.13%	44.33%	NA
All Indica	2759	30.20%	2.70%	9.28%	57.77%	NA
All Japonica	1512	71.70%	0.70%	6.22%	21.36%	NA
Aus	269	38.30%	4.80%	6.32%	50.56%	NA
Indica I	595	0.30%	2.90%	10.59%	86.22%	NA
Indica II	465	20.60%	4.10%	7.96%	67.31%	NA
Indica III	913	54.70%	2.00%	9.31%	34.06%	NA
Indica Intermediate	786	30.20%	2.70%	9.03%	58.14%	NA
Temperate Japonica	767	93.50%	0.40%	0.91%	5.22%	NA
Tropical Japonica	504	38.30%	1.60%	15.48%	44.64%	NA
Japonica Intermediate	241	72.20%	0.00%	3.73%	24.07%	NA
VI/Aromatic	96	86.50%	2.10%	4.17%	7.29%	NA
Intermediate	90	46.70%	0.00%	14.44%	38.89%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0502283394	C -> DEL	N	N	silent_mutation	Average:15.904; most accessible tissue: Minghui63 young leaf, score: 21.268	N	N	N	N
vg0502283394	C -> A	LOC_Os05g04790.1	downstream_gene_variant ; 3346.0bp to feature; MODIFIER	silent_mutation	Average:15.904; most accessible tissue: Minghui63 young leaf, score: 21.268	N	N	N	N
vg0502283394	C -> A	LOC_Os05g04790-LOC_Os05g04810	intergenic_region ; MODIFIER	silent_mutation	Average:15.904; most accessible tissue: Minghui63 young leaf, score: 21.268	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0502283394	NA	6.11E-06	mr1120	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
vg0502283394	NA	9.54E-07	mr1045_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
vg0502283394	3.83E-06	3.69E-06	mr1109_2	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
vg0502283394	NA	9.78E-06	mr1112_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
vg0502283394	NA	4.49E-08	mr1423_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
vg0502283394	NA	3.81E-06	mr1754_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
vg0502283394	NA	5.42E-06	mr1763_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
vg0502283394	NA	3.33E-06	mr1785_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
vg0502283394	NA	1.95E-08	mr1837_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
vg0502283394	NA	3.44E-11	mr1844_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
vg0502283394	NA	3.25E-06	mr1915_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
vg0502283394	NA	6.50E-06	mr1957_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