Search for Variation information by Variation ID:
Detailed information for vg1001933318:
| Variant ID: vg1001933318 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 1933318 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
TTTTGGTCGGTCGCTAGCATCTTGAAAAGGTAGCTGTACTCCTCCTGTGATAAACTATTTAGATGAACTGCCTTTGCTGTTCCGAACCTTGCAAGATTTT[C/T]
AATCCTACTTATGATTACCACTTTGCTTCCTCCAGCTGTCATCTGACTTACAGTAGAATAGAAGTTTACCCAATCATTTTCATCTATGTCCGTAAAATAT
Reverse complement sequence
ATATTTTACGGACATAGATGAAAATGATTGGGTAAACTTCTATTCTACTGTAAGTCAGATGACAGCTGGAGGAAGCAAAGTGGTAATCATAAGTAGGATT[G/A]
AAAATCTTGCAAGGTTCGGAACAGCAAAGGCAGTTCATCTAAATAGTTTATCACAGGAGGAGTACAGCTACCTTTTCAAGATGCTAGCGACCGACCAAAA
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 | 84.70% | 0.20% | 0.51% | 14.56% | NA |
| All Indica | 2759 | 77.90% | 0.30% | 0.65% | 21.17% | NA |
| All Japonica | 1512 | 99.50% | 0.00% | 0.00% | 0.46% | NA |
| Aus | 269 | 65.40% | 0.00% | 2.23% | 32.34% | NA |
| Indica I | 595 | 61.20% | 0.00% | 0.50% | 38.32% | NA |
| Indica II | 465 | 85.60% | 0.00% | 0.22% | 14.19% | NA |
| Indica III | 913 | 80.30% | 0.40% | 0.55% | 18.73% | NA |
| Indica Intermediate | 786 | 83.10% | 0.60% | 1.15% | 15.14% | NA |
| Temperate Japonica | 767 | 99.30% | 0.00% | 0.00% | 0.65% | NA |
| Tropical Japonica | 504 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 99.20% | 0.00% | 0.00% | 0.83% | NA |
| VI/Aromatic | 96 | 95.80% | 0.00% | 0.00% | 4.17% | NA |
| Intermediate | 90 | 93.30% | 0.00% | 0.00% | 6.67% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1001933318 | C -> T | LOC_Os10g04160.1 | missense_variant ; p.Glu189Lys; MODERATE | nonsynonymous_codon ; E189K | Average:40.827; most accessible tissue: Callus, score: 77.054 | benign  |
1.399 |
TOLERATED | 0.23 |
| vg1001933318 | C -> DEL | LOC_Os10g04160.1 | N | frameshift_variant | Average:40.827; most accessible tissue: Callus, score: 77.054 | N | N | N | N |