Search for Variation information by Variation ID:

Please input a variation ID (e.g., vg0722097923 , STR0500036000 ).

Detailed information for vg0139404590:

Variant ID: vg0139404590 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 39404590
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.01, others allele: 0.00, population size: 117. )

Flanking Sequence (100 bp) in Reference Genome:

GCCGGCCATTGCTTGGAGGAAATCAGCGTCAGCACGGTGCGAATGGTCGCTGGTTTGACGACGGGCGAGAATGTCTCGCCAAAGTCGACGCCCGGGCGCT[G/A]
GTTAAACCCGCGAACCACCCAACGTGCCTTGTACTTGTCGAGTGAGCCGTCAGCATGAAGCTTGGTCTTGAAGACCCACTTGCCGGTGATGATCCGAGCA

Reverse complement sequence

TGCTCGGATCATCACCGGCAAGTGGGTCTTCAAGACCAAGCTTCATGCTGACGGCTCACTCGACAAGTACAAGGCACGTTGGGTGGTTCGCGGGTTTAAC[C/T]
AGCGCCCGGGCGTCGACTTTGGCGAGACATTCTCGCCCGTCGTCAAACCAGCGACCATTCGCACCGTGCTGACGCTGATTTCCTCCAAGCAATGGCCGGC

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	25.30%	0.10%	4.85%	69.72%	NA
All Indica	2759	1.40%	0.00%	2.21%	96.38%	NA
All Japonica	1512	74.50%	0.40%	10.45%	14.62%	NA
Aus	269	0.00%	0.00%	0.00%	100.00%	NA
Indica I	595	2.70%	0.00%	2.86%	94.45%	NA
Indica II	465	0.60%	0.00%	0.43%	98.92%	NA
Indica III	913	0.20%	0.00%	1.75%	98.03%	NA
Indica Intermediate	786	2.30%	0.00%	3.31%	94.40%	NA
Temperate Japonica	767	85.70%	0.00%	11.73%	2.61%	NA
Tropical Japonica	504	57.30%	0.20%	9.72%	32.74%	NA
Japonica Intermediate	241	75.10%	2.10%	7.88%	14.94%	NA
VI/Aromatic	96	1.00%	0.00%	0.00%	98.96%	NA
Intermediate	90	32.20%	0.00%	11.11%	56.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0139404590	G -> A	LOC_Os01g67800.1	stop_gained ; p.Gln966*; HIGH	stop_gained	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N
vg0139404590	G -> DEL	LOC_Os01g67800.1	N	frameshift_variant	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N