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Detailed information for vg0409861333:

Variant ID: vg0409861333 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 9861333
Reference Allele: C	Alternative Allele: A
Primary Allele: C	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CACACGTGGGTGCGATCTTTTTGACCGGAATGAAAAAGTTCAAAAAGCACTAAAACAATATTTTCGCACATATTATAGTGTATTGGGTGCAATCATTGAA[C/A]
AAAGTCACTTCCTGATTCGCGCAGCCATCTTTTGTCAATTAATGCCAATATTAGGATACACATGTGGGTGTGATGTTTTTGACCGGAATGAAAAAGATCA

Reverse complement sequence

TGATCTTTTTCATTCCGGTCAAAAACATCACACCCACATGTGTATCCTAATATTGGCATTAATTGACAAAAGATGGCTGCGCGAATCAGGAAGTGACTTT[G/T]
TTCAATGATTGCACCCAATACACTATAATATGTGCGAAAATATTGTTTTAGTGCTTTTTGAACTTTTTCATTCCGGTCAAAAAGATCGCACCCACGTGTG

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	37.20%	0.20%	39.65%	23.00%	NA
All Indica	2759	28.30%	0.30%	54.22%	17.18%	NA
All Japonica	1512	61.20%	0.00%	4.96%	33.80%	NA
Aus	269	5.90%	0.40%	88.85%	4.83%	NA
Indica I	595	39.70%	0.00%	42.18%	18.15%	NA
Indica II	465	26.00%	0.20%	58.49%	15.27%	NA
Indica III	913	27.60%	0.30%	55.64%	16.43%	NA
Indica Intermediate	786	22.00%	0.40%	59.16%	18.45%	NA
Temperate Japonica	767	96.00%	0.00%	0.52%	3.52%	NA
Tropical Japonica	504	4.60%	0.00%	11.51%	83.93%	NA
Japonica Intermediate	241	69.30%	0.00%	5.39%	25.31%	NA
VI/Aromatic	96	2.10%	0.00%	29.17%	68.75%	NA
Intermediate	90	33.30%	1.10%	40.00%	25.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0409861333	C -> DEL	N	N	silent_mutation	Average:23.621; most accessible tissue: Minghui63 panicle, score: 56.842	N	N	N	N
vg0409861333	C -> A	LOC_Os04g17930.1	upstream_gene_variant ; 4118.0bp to feature; MODIFIER	silent_mutation	Average:23.621; most accessible tissue: Minghui63 panicle, score: 56.842	N	N	N	N
vg0409861333	C -> A	LOC_Os04g17940.1	downstream_gene_variant ; 1067.0bp to feature; MODIFIER	silent_mutation	Average:23.621; most accessible tissue: Minghui63 panicle, score: 56.842	N	N	N	N
vg0409861333	C -> A	LOC_Os04g17930-LOC_Os04g17940	intergenic_region ; MODIFIER	silent_mutation	Average:23.621; most accessible tissue: Minghui63 panicle, score: 56.842	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0409861333	NA	6.13E-06	mr1111	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
vg0409861333	NA	7.27E-07	mr1690	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
vg0409861333	NA	4.70E-42	mr1719	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
vg0409861333	NA	1.92E-70	mr1019_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