Search for Variation information by Variation ID:

Please input a variation ID (e.g., vg0722097923).

Detailed information for vg1005451907:

Variant ID: vg1005451907 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 5451907
Reference Allele: A	Alternative Allele: G
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CTAATGACAGATTATTTGGGCTTAATAAATTCACCTCGCAGTTTCTAGGCGGAATCTGTAATTTGTTTTGTTATTAGTCCATGTTTAATATTTCAAATAT[A/G]
TATGTGTATATCCGATGTGACACGCCAAAATTTTCATGCATGACCTAAACATGCCCTAACTTGTGAAATGAAGTTATTTCTTCAAAATATTTAGTTGCAA

Reverse complement sequence

TTGCAACTAAATATTTTGAAGAAATAACTTCATTTCACAAGTTAGGGCATGTTTAGGTCATGCATGAAAATTTTGGCGTGTCACATCGGATATACACATA[T/C]
ATATTTGAAATATTAAACATGGACTAATAACAAAACAAATTACAGATTCCGCCTAGAAACTGCGAGGTGAATTTATTAAGCCCAAATAATCTGTCATTAG

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	78.60%	21.40%	0.02%	0.00%	NA
All Indica	2759	98.80%	1.20%	0.04%	0.00%	NA
All Japonica	1512	38.60%	61.40%	0.00%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	99.50%	0.50%	0.00%	0.00%	NA
Indica II	465	99.10%	0.90%	0.00%	0.00%	NA
Indica III	913	98.50%	1.50%	0.00%	0.00%	NA
Indica Intermediate	786	98.50%	1.40%	0.13%	0.00%	NA
Temperate Japonica	767	26.60%	73.40%	0.00%	0.00%	NA
Tropical Japonica	504	50.60%	49.40%	0.00%	0.00%	NA
Japonica Intermediate	241	51.90%	48.10%	0.00%	0.00%	NA
VI/Aromatic	96	77.10%	22.90%	0.00%	0.00%	NA
Intermediate	90	68.90%	31.10%	0.00%	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
vg1005451907	A -> G	LOC_Os10g10030.1	upstream_gene_variant ; 2833.0bp to feature; MODIFIER	silent_mutation	Average:28.407; most accessible tissue: Minghui63 root, score: 52.955	N	N	N	N
vg1005451907	A -> G	LOC_Os10g10030-LOC_Os10g10040	intergenic_region ; MODIFIER	silent_mutation	Average:28.407; most accessible tissue: Minghui63 root, score: 52.955	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1005451907	8.72E-15	4.98E-28	mr1768	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
vg1005451907	4.83E-07	1.20E-10	mr1768	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
vg1005451907	8.99E-22	6.39E-47	mr1768_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
vg1005451907	1.04E-08	7.34E-12	mr1768_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