Search for Variation information by Variation ID:
Detailed information for vg0221511095:
| Variant ID: vg0221511095 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 21511095 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
GATGCTTTATGCTATCCTGATAACTTCGAGGAAGTTGCGCCATTATTTCCAGGCGCATCGGGTCACGGTGGTTACGTCTTATCCCCTCGGCCAAATCTTG[T/C]
ATAACCGAGAGGGTACTGGACGGGTGGTGAAATGGGCAATCGAACTCTCTGAATTCGATTTGCGCTTGAAACCAAGCCACGCGATCAAGAGCCAGGCCCT
Reverse complement sequence
AGGGCCTGGCTCTTGATCGCGTGGCTTGGTTTCAAGCGCAAATCGAATTCAGAGAGTTCGATTGCCCATTTCACCACCCGTCCAGTACCCTCTCGGTTAT[A/G]
CAAGATTTGGCCGAGGGGATAAGACGTAACCACCGTGACCCGATGCGCCTGGAAATAATGGCGCAACTTCCTCGAAGTTATCAGGATAGCATAAAGCATC
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 | 35.70% | 0.20% | 0.91% | 63.20% | NA |
| All Indica | 2759 | 2.70% | 0.40% | 1.30% | 95.58% | NA |
| All Japonica | 1512 | 97.00% | 0.00% | 0.07% | 2.98% | NA |
| Aus | 269 | 0.40% | 0.00% | 1.12% | 98.51% | NA |
| Indica I | 595 | 1.80% | 0.00% | 1.85% | 96.30% | NA |
| Indica II | 465 | 3.90% | 0.00% | 1.51% | 94.62% | NA |
| Indica III | 913 | 2.00% | 1.10% | 0.77% | 96.17% | NA |
| Indica Intermediate | 786 | 3.60% | 0.10% | 1.40% | 94.91% | NA |
| Temperate Japonica | 767 | 99.20% | 0.00% | 0.13% | 0.65% | NA |
| Tropical Japonica | 504 | 93.10% | 0.00% | 0.00% | 6.94% | NA |
| Japonica Intermediate | 241 | 97.90% | 0.00% | 0.00% | 2.07% | NA |
| VI/Aromatic | 96 | 91.70% | 0.00% | 0.00% | 8.33% | NA |
| Intermediate | 90 | 61.10% | 0.00% | 3.33% | 35.56% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0221511095 | T -> DEL | LOC_Os02g35800.1 | N | frameshift_variant | Average:6.464; most accessible tissue: Zhenshan97 panicle, score: 16.188 | N | N | N | N |
| vg0221511095 | T -> C | LOC_Os02g35800.1 | missense_variant ; p.Tyr703His; MODERATE | nonsynonymous_codon ; Y703H | Average:6.464; most accessible tissue: Zhenshan97 panicle, score: 16.188 | benign  |
-0.31 |
TOLERATED | 1.00 |