Search for Variation information by Variation ID:
Detailed information for vg0620131984:
| Variant ID: vg0620131984 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 20131984 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
GTGGCGGCCAAGATCCCGGAGTTCGCGTACGCGGGGTCGGCGAGGCACGGCGGCGGCGGCGAGTGCTCGGTGTGCCTCGGCGCGGTGCAGGGCGGCGAGG[C/T]
GGTGCGGCGGCTGCCGGCGTGCAAGCACCTGTACCACGTGGAGTGCATCGACATGTGGCTGGCCTCGCACGCCACGTGCCCAATCTGCCGGACGGAGGTC
Reverse complement sequence
GACCTCCGTCCGGCAGATTGGGCACGTGGCGTGCGAGGCCAGCCACATGTCGATGCACTCCACGTGGTACAGGTGCTTGCACGCCGGCAGCCGCCGCACC[G/A]
CCTCGCCGCCCTGCACCGCGCCGAGGCACACCGAGCACTCGCCGCCGCCGCCGTGCCTCGCCGACCCCGCGTACGCGAACTCCGGGATCTTGGCCGCCAC
Allele Frequencies:
| Populations | Population Size | Frequency of C(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 72.20% | 8.40% | 13.27% | 6.12% | NA |
| All Indica | 2759 | 79.40% | 0.40% | 13.30% | 6.89% | NA |
| All Japonica | 1512 | 54.60% | 22.50% | 16.67% | 6.28% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 69.90% | 0.00% | 22.52% | 7.56% | NA |
| Indica II | 465 | 66.70% | 1.50% | 15.05% | 16.77% | NA |
| Indica III | 913 | 92.00% | 0.10% | 6.46% | 1.42% | NA |
| Indica Intermediate | 786 | 79.60% | 0.30% | 13.23% | 6.87% | NA |
| Temperate Japonica | 767 | 50.50% | 12.00% | 26.99% | 10.56% | NA |
| Tropical Japonica | 504 | 68.70% | 23.60% | 5.75% | 1.98% | NA |
| Japonica Intermediate | 241 | 38.20% | 53.50% | 6.64% | 1.66% | NA |
| VI/Aromatic | 96 | 65.60% | 34.40% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 72.20% | 14.40% | 8.89% | 4.44% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0620131984 | C -> T | LOC_Os06g34620.1 | missense_variant ; p.Ala114Val; MODERATE | nonsynonymous_codon ; A114V | Average:72.322; most accessible tissue: Zhenshan97 panicle, score: 84.824 | benign  |
-0.941 |
TOLERATED | 0.76 |
| vg0620131984 | C -> DEL | LOC_Os06g34620.1 | N | frameshift_variant | Average:72.322; most accessible tissue: Zhenshan97 panicle, score: 84.824 | N | N | N | N |