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Detailed information for vg0704183155:

Variant ID: vg0704183155 (JBrowse)Variation Type: INDEL
Chromosome: chr07Position: 4183155
Reference Allele: GAAlternative Allele: G,GAA
Primary Allele: GASecondary Allele: GAA

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


AATTTAACAGGTATTTTCTTTCATTGATACAGAAATCTATACATCAATATCAATTCAAGGATATGCAATGACAAAATAATGGCATTAGTTGATGATAGAT[GA/G,GAA]
AAAAAAATGTTATTGTACAGTTCACATGTGAAGTGTAACACATTCACATTAGCAAAGAGAAAATTCTTGACCAAACTTAAGTTGTGCCCACACATACCGT

Reverse complement sequence

ACGGTATGTGTGGGCACAACTTAAGTTTGGTCAAGAATTTTCTCTTTGCTAATGTGAATGTGTTACACTTCACATGTGAACTGTACAATAACATTTTTTT[TC/C,TTC]
ATCTATCATCAACTAATGCCATTATTTTGTCATTGCATATCCTTGAATTGATATTGATGTATAGATTTCTGTATCAATGAAAGAAAATACCTGTTAAATT

Allele Frequencies:

Populations Population SizeFrequency of GA(primary allele) Frequency of GAA(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 99.80% 0.10% 0.02% 0.00% G: 0.06%
All Indica  2759 99.80% 0.20% 0.04% 0.00% NA
All Japonica  1512 99.80% 0.00% 0.00% 0.00% G: 0.20%
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 99.80% 0.00% 0.17% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 99.50% 0.50% 0.00% 0.00% NA
Indica Intermediate  786 100.00% 0.00% 0.00% 0.00% NA
Temperate Japonica  767 99.60% 0.00% 0.00% 0.00% G: 0.39%
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 100.00% 0.00% 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
vg0704183155 GA -> GAA LOC_Os07g08190.1 downstream_gene_variant ; 1508.0bp to feature; MODIFIER N Average:58.556; most accessible tissue: Minghui63 flag leaf, score: 77.153 N N N N
vg0704183155 GA -> GAA LOC_Os07g08210.1 downstream_gene_variant ; 2048.0bp to feature; MODIFIER N Average:58.556; most accessible tissue: Minghui63 flag leaf, score: 77.153 N N N N
vg0704183155 GA -> GAA LOC_Os07g08210.3 downstream_gene_variant ; 2048.0bp to feature; MODIFIER N Average:58.556; most accessible tissue: Minghui63 flag leaf, score: 77.153 N N N N
vg0704183155 GA -> GAA LOC_Os07g08210.2 downstream_gene_variant ; 2048.0bp to feature; MODIFIER N Average:58.556; most accessible tissue: Minghui63 flag leaf, score: 77.153 N N N N
vg0704183155 GA -> GAA LOC_Os07g08200.1 intron_variant ; MODIFIER N Average:58.556; most accessible tissue: Minghui63 flag leaf, score: 77.153 N N N N
vg0704183155 GA -> G LOC_Os07g08190.1 downstream_gene_variant ; 1507.0bp to feature; MODIFIER N Average:58.556; most accessible tissue: Minghui63 flag leaf, score: 77.153 N N N N
vg0704183155 GA -> G LOC_Os07g08210.1 downstream_gene_variant ; 2049.0bp to feature; MODIFIER N Average:58.556; most accessible tissue: Minghui63 flag leaf, score: 77.153 N N N N
vg0704183155 GA -> G LOC_Os07g08210.3 downstream_gene_variant ; 2049.0bp to feature; MODIFIER N Average:58.556; most accessible tissue: Minghui63 flag leaf, score: 77.153 N N N N
vg0704183155 GA -> G LOC_Os07g08210.2 downstream_gene_variant ; 2049.0bp to feature; MODIFIER N Average:58.556; most accessible tissue: Minghui63 flag leaf, score: 77.153 N N N N
vg0704183155 GA -> G LOC_Os07g08200.1 intron_variant ; MODIFIER N Average:58.556; most accessible tissue: Minghui63 flag leaf, score: 77.153 N N N N