Search for Variation information by Variation ID:
Detailed information for vg0100791480:
| Variant ID: vg0100791480 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 791480 |
| Reference Allele: C | Alternative Allele: A |
| Primary Allele: C | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
GTGGGCACAACAATCTATCTTTCACTAAAGACAAGATATAATGAAGAGATACATTTGAAGGTCGAAATGTTTCTCAAGACATATGGCACATCGAAACCCA[C/A]
AAGGTATAGTTTCTCTGAAGTTAAGAAGATTACAAGACGGTTCAGGGAAAAGATAGGCCACGGTGGGTATGGAAATGTATACAAGGGTGAGCTACCAAAT
Reverse complement sequence
ATTTGGTAGCTCACCCTTGTATACATTTCCATACCCACCGTGGCCTATCTTTTCCCTGAACCGTCTTGTAATCTTCTTAACTTCAGAGAAACTATACCTT[G/T]
TGGGTTTCGATGTGCCATATGTCTTGAGAAACATTTCGACCTTCAAATGTATCTCTTCATTATATCTTGTCTTTAGTGAAAGATAGATTGTTGTGCCCAC
Allele Frequencies:
| Populations | Population Size | Frequency of C(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 56.30% | 1.20% | 2.07% | 40.41% | NA |
| All Indica | 2759 | 50.20% | 1.40% | 2.46% | 45.89% | NA |
| All Japonica | 1512 | 73.10% | 0.10% | 1.12% | 25.66% | NA |
| Aus | 269 | 36.40% | 5.20% | 1.86% | 56.51% | NA |
| Indica I | 595 | 69.20% | 0.70% | 0.50% | 29.58% | NA |
| Indica II | 465 | 75.90% | 0.00% | 1.08% | 23.01% | NA |
| Indica III | 913 | 18.70% | 3.10% | 2.85% | 75.36% | NA |
| Indica Intermediate | 786 | 57.30% | 0.90% | 4.33% | 37.53% | NA |
| Temperate Japonica | 767 | 70.30% | 0.30% | 1.43% | 28.03% | NA |
| Tropical Japonica | 504 | 83.10% | 0.00% | 0.40% | 16.47% | NA |
| Japonica Intermediate | 241 | 61.00% | 0.00% | 1.66% | 37.34% | NA |
| VI/Aromatic | 96 | 10.40% | 0.00% | 5.21% | 84.38% | NA |
| Intermediate | 90 | 71.10% | 0.00% | 3.33% | 25.56% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0100791480 | C -> A | LOC_Os01g02440.1 | missense_variant ; p.Thr252Lys; MODERATE | nonsynonymous_codon ; T252K | Average:54.274; most accessible tissue: Zhenshan97 panicle, score: 68.538 | benign  |
0.981 |
DELETERIOUS | 0.03 |
| vg0100791480 | C -> DEL | LOC_Os01g02440.1 | N | frameshift_variant | Average:54.274; most accessible tissue: Zhenshan97 panicle, score: 68.538 | N | N | N | N |