Search for Variation information by Variation ID:
Detailed information for vg0128724307:
| Variant ID: vg0128724307 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 28724307 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
GACCGGTCATTCTTGTCCACCACGTGTCAGTTTAGCATGTCGCACGTCTGTCCTTCTTCATACAATGACTTCTTTGCAATGGTTGCGATGAAGCCTGGAA[T/C]
GTATCTAGCCGGGACTGGCGTGCTAACTCCAGGAGTTAGCACACCGGCTCCGGCTAGGGACGAGTGCCTGGAGGCTCTCATCATTCCGACGGGACGGGGC
Reverse complement sequence
GCCCCGTCCCGTCGGAATGATGAGAGCCTCCAGGCACTCGTCCCTAGCCGGAGCCGGTGTGCTAACTCCTGGAGTTAGCACGCCAGTCCCGGCTAGATAC[A/G]
TTCCAGGCTTCATCGCAACCATTGCAAAGAAGTCATTGTATGAAGAAGGACAGACGTGCGACATGCTAAACTGACACGTGGTGGACAAGAATGACCGGTC
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 | 30.50% | 0.30% | 9.54% | 59.69% | NA |
| All Indica | 2759 | 2.50% | 0.40% | 15.26% | 81.77% | NA |
| All Japonica | 1512 | 85.40% | 0.00% | 0.07% | 14.48% | NA |
| Aus | 269 | 5.20% | 0.00% | 6.32% | 88.48% | NA |
| Indica I | 595 | 1.30% | 0.00% | 3.53% | 95.13% | NA |
| Indica II | 465 | 3.20% | 0.00% | 12.47% | 84.30% | NA |
| Indica III | 913 | 2.40% | 0.80% | 26.40% | 70.43% | NA |
| Indica Intermediate | 786 | 3.20% | 0.60% | 12.85% | 83.33% | NA |
| Temperate Japonica | 767 | 99.30% | 0.00% | 0.00% | 0.65% | NA |
| Tropical Japonica | 504 | 60.90% | 0.00% | 0.00% | 39.09% | NA |
| Japonica Intermediate | 241 | 92.50% | 0.00% | 0.41% | 7.05% | NA |
| VI/Aromatic | 96 | 21.90% | 0.00% | 9.38% | 68.75% | NA |
| Intermediate | 90 | 50.00% | 0.00% | 3.33% | 46.67% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0128724307 | T -> DEL | LOC_Os01g49990.1 | N | frameshift_variant | Average:15.596; most accessible tissue: Zhenshan97 panicle, score: 24.575 | N | N | N | N |
| vg0128724307 | T -> C | LOC_Os01g49990.1 | missense_variant ; p.Met67Thr; MODERATE | nonsynonymous_codon ; M67T | Average:15.596; most accessible tissue: Zhenshan97 panicle, score: 24.575 | benign  |
-0.122 |
TOLERATED | 0.05 |