Search for Variation information by Variation ID:
Detailed information for vg0319758657:
| Variant ID: vg0319758657 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 19758657 |
| Reference Allele: A | Alternative Allele: T |
| Primary Allele: A | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
TATTCTGGTTGAAACCTTGGGGAGACTTCTCATCTTCATCATCTGAGGAGACTTGATCTGAATCTTCATTATCAGACACTCTACCTCCATTAGCTAAAAG[A/T]
TGCTCTGTCAACTGTGGCGCACCTCGGAAGGTATTTCTTCTCTGACGTTTTGTCATTCCTGGTGGAGGCCATTCTGTGCTGGTAATGCTCATCTTACGGA
Reverse complement sequence
TCCGTAAGATGAGCATTACCAGCACAGAATGGCCTCCACCAGGAATGACAAAACGTCAGAGAAGAAATACCTTCCGAGGTGCGCCACAGTTGACAGAGCA[T/A]
CTTTTAGCTAATGGAGGTAGAGTGTCTGATAATGAAGATTCAGATCAAGTCTCCTCAGATGATGAAGATGAGAAGTCTCCCCAAGGTTTCAACCAGAATA
Allele Frequencies:
| Populations | Population Size | Frequency of A(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 31.20% | 0.30% | 2.67% | 65.85% | NA |
| All Indica | 2759 | 2.90% | 0.10% | 1.59% | 95.36% | NA |
| All Japonica | 1512 | 82.80% | 0.60% | 5.22% | 11.38% | NA |
| Aus | 269 | 10.00% | 0.00% | 0.00% | 89.96% | NA |
| Indica I | 595 | 2.50% | 0.00% | 2.35% | 95.13% | NA |
| Indica II | 465 | 3.70% | 0.00% | 0.65% | 95.70% | NA |
| Indica III | 913 | 1.90% | 0.20% | 1.10% | 96.82% | NA |
| Indica Intermediate | 786 | 4.10% | 0.10% | 2.16% | 93.64% | NA |
| Temperate Japonica | 767 | 93.60% | 0.50% | 5.48% | 0.39% | NA |
| Tropical Japonica | 504 | 65.50% | 0.40% | 3.77% | 30.36% | NA |
| Japonica Intermediate | 241 | 84.60% | 1.20% | 7.47% | 6.64% | NA |
| VI/Aromatic | 96 | 74.00% | 0.00% | 1.04% | 25.00% | NA |
| Intermediate | 90 | 50.00% | 0.00% | 2.22% | 47.78% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0319758657 | A -> T | LOC_Os03g35670.1 | missense_variant ; p.His163Gln; MODERATE | nonsynonymous_codon ; H163Q | Average:5.354; most accessible tissue: Callus, score: 12.211 | possibly damaging  |
1.729 |
DELETERIOUS | 0.00 |
| vg0319758657 | A -> DEL | LOC_Os03g35670.1 | N | frameshift_variant | Average:5.354; most accessible tissue: Callus, score: 12.211 | N | N | N | N |