Search for Variation information by Variation ID:
Detailed information for vg0719563095:
| Variant ID: vg0719563095 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 19563095 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
AATAAGCACGAAGGAGAAGAAGTTCACAAACCTAAAGTCTCATGACTGTCACGTGTTGATGACACAACTGCTACCAGTTGTAATAAGGGGTATCCTTCCA[G/A]
ACAATGTGTAACATCCTGAAAATTCAAGACAATAAAAATCACTAAAATTTTGAACTTTTTAAAACTTTTGCATCATGCTGGTTGTTATGATTGCTATTGC
Reverse complement sequence
GCAATAGCAATCATAACAACCAGCATGATGCAAAAGTTTTAAAAAGTTCAAAATTTTAGTGATTTTTATTGTCTTGAATTTTCAGGATGTTACACATTGT[C/T]
TGGAAGGATACCCCTTATTACAACTGGTAGCAGTTGTGTCATCAACACGTGACAGTCATGAGACTTTAGGTTTGTGAACTTCTTCTCCTTCGTGCTTATT
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 | 25.10% | 7.00% | 28.23% | 39.76% | NA |
| All Indica | 2759 | 20.40% | 0.10% | 30.48% | 49.00% | NA |
| All Japonica | 1512 | 37.90% | 21.40% | 19.05% | 21.63% | NA |
| Aus | 269 | 9.70% | 0.00% | 62.08% | 28.25% | NA |
| Indica I | 595 | 2.70% | 0.00% | 21.34% | 75.97% | NA |
| Indica II | 465 | 20.20% | 0.00% | 18.92% | 60.86% | NA |
| Indica III | 913 | 32.50% | 0.00% | 45.02% | 22.45% | NA |
| Indica Intermediate | 786 | 20.00% | 0.30% | 27.35% | 52.42% | NA |
| Temperate Japonica | 767 | 55.10% | 37.90% | 2.87% | 4.04% | NA |
| Tropical Japonica | 504 | 10.30% | 0.80% | 48.41% | 40.48% | NA |
| Japonica Intermediate | 241 | 40.70% | 12.00% | 9.13% | 38.17% | NA |
| VI/Aromatic | 96 | 3.10% | 0.00% | 10.42% | 86.46% | NA |
| Intermediate | 90 | 20.00% | 3.30% | 31.11% | 45.56% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0719563095 | G -> DEL | LOC_Os07g32740.1 | N | frameshift_variant | Average:8.219; most accessible tissue: Zhenshan97 root, score: 12.891 | N | N | N | N |
| vg0719563095 | G -> A | LOC_Os07g32740.1 | missense_variant ; p.Asp638Asn; MODERATE | nonsynonymous_codon ; D638N | Average:8.219; most accessible tissue: Zhenshan97 root, score: 12.891 | benign  |
0.745 |
DELETERIOUS | 0.01 |