Search for Variation information by Variation ID:

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

Detailed information for vg0409515128:

Variant ID: vg0409515128 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 9515128
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CGGCCATCTCAAGACGATGTAAAACACATCGGCTGTCATGCATCAGCAACACTAGCCGATCATGCGTCAACCCAAACACTTGGGTAATACTTCTTCAAGT[A/G]
TTTGCCATTGAGCGCCCATCCATAAACCTCACCATCAAGCCCTTGCAACATATATGCCCCTTTAGACACAACATTATAGATTTGAAACGGTCCTTCCCAA

Reverse complement sequence

TTGGGAAGGACCGTTTCAAATCTATAATGTTGTGTCTAAAGGGGCATATATGTTGCAAGGGCTTGATGGTGAGGTTTATGGATGGGCGCTCAATGGCAAA[T/C]
ACTTGAAGAAGTATTACCCAAGTGTTTGGGTTGACGCATGATCGGCTAGTGTTGCTGATGCATGACAGCCGATGTGTTTTACATCGTCTTGAGATGGCCG

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 91.10% 0.10% 0.83% 8.00% NA
All Indica  2759 99.90% 0.00% 0.04% 0.00% NA
All Japonica  1512 74.10% 0.10% 2.12% 23.74% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 99.80% 0.00% 0.22% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 99.90% 0.10% 0.00% 0.00% NA
Temperate Japonica  767 98.60% 0.00% 0.00% 1.43% NA
Tropical Japonica  504 33.70% 0.00% 5.36% 60.91% NA
Japonica Intermediate  241 80.50% 0.40% 2.07% 17.01% NA
VI/Aromatic  96 75.00% 1.00% 5.21% 18.75% NA
Intermediate  90 97.80% 0.00% 1.11% 1.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0409515128 A -> DEL LOC_Os04g17380.1 N frameshift_variant Average:37.548; most accessible tissue: Minghui63 young leaf, score: 63.571 N N N N
vg0409515128 A -> G LOC_Os04g17380.1 missense_variant ; p.Tyr160His; MODERATE nonsynonymous_codon ; Y160H Average:37.548; most accessible tissue: Minghui63 young leaf, score: 63.571 probably damaging 2.485 TOLERATED 0.09