Search for Variation information by Variation ID:

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

Detailed information for vg0430653744:

Variant ID: vg0430653744 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 30653744
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: Unkown

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 395. )

Flanking Sequence (100 bp) in Reference Genome:


CTTCGCAGTAGTCGCCGAAGAGTTCACTAGTGAATTGGGTGCCATTATCCGTAATGATACGGTTAGGCACTCCAAAACGGGCCGTGATGCCCTTAATGAA[T/C]
TTAAGTGCAGAGTGCTTATCGATCTTGACGACCGGATAAGCCTCGGGCCACTTAGTGAACTTGTCGATCGCGACATACAGATACTCAAACCCGCCCGGGG

Reverse complement sequence

CCCCGGGCGGGTTTGAGTATCTGTATGTCGCGATCGACAAGTTCACTAAGTGGCCCGAGGCTTATCCGGTCGTCAAGATCGATAAGCACTCTGCACTTAA[A/G]
TTCATTAAGGGCATCACGGCCCGTTTTGGAGTGCCTAACCGTATCATTACGGATAATGGCACCCAATTCACTAGTGAACTCTTCGGCGACTACTGCGAAG

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of Unkown(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 84.40% 0.00% 0.21% 15.38% NA
All Indica  2759 99.30% 0.00% 0.00% 0.69% NA
All Japonica  1512 55.80% 0.00% 0.53% 43.72% NA
Aus  269 91.40% 0.00% 0.74% 7.81% NA
Indica I  595 99.80% 0.00% 0.00% 0.17% NA
Indica II  465 99.40% 0.00% 0.00% 0.65% NA
Indica III  913 99.90% 0.00% 0.00% 0.11% NA
Indica Intermediate  786 98.20% 0.00% 0.00% 1.78% NA
Temperate Japonica  767 64.90% 0.00% 0.26% 34.81% NA
Tropical Japonica  504 46.20% 0.00% 0.60% 53.17% NA
Japonica Intermediate  241 46.50% 0.00% 1.24% 52.28% NA
VI/Aromatic  96 81.20% 0.00% 0.00% 18.75% NA
Intermediate  90 91.10% 0.00% 0.00% 8.89% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0430653744 T -> C LOC_Os04g51730.1 synonymous_variant ; p.Lys206Lys; LOW N Average:11.428; most accessible tissue: Minghui63 panicle, score: 20.733 N N N N
vg0430653744 T -> C LOC_Os04g51720.1 downstream_gene_variant ; 1346.0bp to feature; MODIFIER N Average:11.428; most accessible tissue: Minghui63 panicle, score: 20.733 N N N N
vg0430653744 T -> C LOC_Os04g51740.1 downstream_gene_variant ; 3635.0bp to feature; MODIFIER N Average:11.428; most accessible tissue: Minghui63 panicle, score: 20.733 N N N N