Search for Variation information by Variation ID:

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

Detailed information for vg0424400921:

Variant ID: vg0424400921 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 24400921
Reference Allele: AAlternative Allele: C
Primary Allele: ASecondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.98, A: 0.02, others allele: 0.00, population size: 300. )

Flanking Sequence (100 bp) in Reference Genome:


ATTAGCCTGAGGTACCTGCTTAGCTTTGAGGTAAGCATGAATAAGTGCAGTATATGTCACCACAGTTGGGGAGCAACCCACACTCCTCATCTCCTCAAAC[A/C]
ACCACTGGGCTTGTTCAATGAGTCCAGCTTTACAAAAGCTGTCAATCAAAATTGTGTATGTATACACATCAGGAGTTACACCGACCATCTTCATCTCTTG

Reverse complement sequence

CAAGAGATGAAGATGGTCGGTGTAACTCCTGATGTGTATACATACACAATTTTGATTGACAGCTTTTGTAAAGCTGGACTCATTGAACAAGCCCAGTGGT[T/G]
GTTTGAGGAGATGAGGAGTGTGGGTTGCTCCCCAACTGTGGTGACATATACTGCACTTATTCATGCTTACCTCAAAGCTAAGCAGGTACCTCAGGCTAAT

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 75.30% 24.60% 0.06% 0.00% NA
All Indica  2759 62.70% 37.20% 0.11% 0.00% NA
All Japonica  1512 99.90% 0.10% 0.00% 0.00% NA
Aus  269 55.80% 44.20% 0.00% 0.00% NA
Indica I  595 73.40% 26.60% 0.00% 0.00% NA
Indica II  465 95.30% 4.50% 0.22% 0.00% NA
Indica III  913 42.10% 57.90% 0.00% 0.00% NA
Indica Intermediate  786 59.30% 40.50% 0.25% 0.00% NA
Temperate Japonica  767 99.90% 0.10% 0.00% 0.00% NA
Tropical Japonica  504 99.80% 0.20% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 99.00% 1.00% 0.00% 0.00% NA
Intermediate  90 83.30% 16.70% 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
vg0424400921 A -> C LOC_Os04g41140.1 missense_variant ; p.Leu514Trp; MODERATE nonsynonymous_codon ; L514W Average:58.575; most accessible tissue: Zhenshan97 young leaf, score: 77.736 unknown nan TOLERATED 1.00