Search for Variation information by Variation ID:
Detailed information for vg0704650378:
| Variant ID: vg0704650378 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 4650378 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.67, T: 0.32, others allele: 0.00, population size: 218. )
Flanking Sequence (100 bp) in Reference Genome:
CCCTCGGCTTTGTTGGTTTTGATGGATGGTGACGGTGTTGCAATAGCAGCTGCGGTAGTTGAGGGTGTGGATGAGTTCATAGTGGCTGGAAACACATGTT[C/T]
TGGTGCAGCAAGAGAACTCTCAACTGCTGGCCTAGTGGTGATGCTGCTTGGTCCCAACGTCAAACACTTGGTGGGCGTCATGTCGACACCGTTCCCGTTG
Reverse complement sequence
CAACGGGAACGGTGTCGACATGACGCCCACCAAGTGTTTGACGTTGGGACCAAGCAGCATCACCACTAGGCCAGCAGTTGAGAGTTCTCTTGCTGCACCA[G/A]
AACATGTGTTTCCAGCCACTATGAACTCATCCACACCCTCAACTACCGCAGCTGCTATTGCAACACCGTCACCATCCATCAAAACCAACAAAGCCGAGGG
Allele Frequencies:
| Populations | Population Size | Frequency of T(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 59.30% | 40.50% | 0.11% | 0.17% | NA |
| All Indica | 2759 | 97.60% | 2.00% | 0.11% | 0.25% | NA |
| All Japonica | 1512 | 0.50% | 99.40% | 0.07% | 0.07% | NA |
| Aus | 269 | 25.30% | 74.70% | 0.00% | 0.00% | NA |
| Indica I | 595 | 99.20% | 0.50% | 0.00% | 0.34% | NA |
| Indica II | 465 | 97.00% | 2.80% | 0.22% | 0.00% | NA |
| Indica III | 913 | 98.10% | 1.40% | 0.11% | 0.33% | NA |
| Indica Intermediate | 786 | 96.20% | 3.40% | 0.13% | 0.25% | NA |
| Temperate Japonica | 767 | 0.50% | 99.30% | 0.13% | 0.00% | NA |
| Tropical Japonica | 504 | 0.40% | 99.60% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 0.40% | 99.20% | 0.00% | 0.41% | NA |
| VI/Aromatic | 96 | 1.00% | 99.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 35.60% | 63.30% | 1.11% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0704650378 | C -> DEL | LOC_Os07g08940.1 | N | frameshift_variant | Average:56.036; most accessible tissue: Zhenshan97 young leaf, score: 73.54 | N | N | N | N |
| vg0704650378 | C -> T | LOC_Os07g08940.1 | missense_variant ; p.Glu60Lys; MODERATE | nonsynonymous_codon ; E60K | Average:56.036; most accessible tissue: Zhenshan97 young leaf, score: 73.54 | benign  |
0.01 |
TOLERATED | 0.14 |