Search for Variation information by Variation ID:
Detailed information for vg0319758680:
| Variant ID: vg0319758680 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 19758680 |
| Reference Allele: C | Alternative Allele: A |
| Primary Allele: C | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
GACTTCTCATCTTCATCATCTGAGGAGACTTGATCTGAATCTTCATTATCAGACACTCTACCTCCATTAGCTAAAAGATGCTCTGTCAACTGTGGCGCAC[C/A]
TCGGAAGGTATTTCTTCTCTGACGTTTTGTCATTCCTGGTGGAGGCCATTCTGTGCTGGTAATGCTCATCTTACGGACTTCATCTTCGGTTCGCATTGGT
Reverse complement sequence
ACCAATGCGAACCGAAGATGAAGTCCGTAAGATGAGCATTACCAGCACAGAATGGCCTCCACCAGGAATGACAAAACGTCAGAGAAGAAATACCTTCCGA[G/T]
GTGCGCCACAGTTGACAGAGCATCTTTTAGCTAATGGAGGTAGAGTGTCTGATAATGAAGATTCAGATCAAGTCTCCTCAGATGATGAAGATGAGAAGTC
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 | 34.70% | 0.10% | 15.45% | 49.70% | NA |
| All Indica | 2759 | 5.30% | 0.00% | 23.23% | 71.51% | NA |
| All Japonica | 1512 | 86.90% | 0.40% | 3.44% | 9.26% | NA |
| Aus | 269 | 18.60% | 0.00% | 8.18% | 73.23% | NA |
| Indica I | 595 | 7.60% | 0.00% | 11.26% | 81.18% | NA |
| Indica II | 465 | 5.20% | 0.00% | 20.65% | 74.19% | NA |
| Indica III | 913 | 2.50% | 0.00% | 32.97% | 64.51% | NA |
| Indica Intermediate | 786 | 6.70% | 0.00% | 22.52% | 70.74% | NA |
| Temperate Japonica | 767 | 98.70% | 0.70% | 0.39% | 0.26% | NA |
| Tropical Japonica | 504 | 67.30% | 0.00% | 7.74% | 25.00% | NA |
| Japonica Intermediate | 241 | 90.50% | 0.40% | 4.15% | 4.98% | NA |
| VI/Aromatic | 96 | 83.30% | 0.00% | 2.08% | 14.58% | NA |
| Intermediate | 90 | 57.80% | 0.00% | 14.44% | 27.78% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0319758680 | C -> A | LOC_Os03g35670.1 | missense_variant ; p.Gly156Cys; MODERATE | nonsynonymous_codon ; G156C | Average:5.944; most accessible tissue: Callus, score: 18.7 | probably damaging  |
3.575 |
DELETERIOUS | 0.00 |
| vg0319758680 | C -> DEL | LOC_Os03g35670.1 | N | frameshift_variant | Average:5.944; most accessible tissue: Callus, score: 18.7 | N | N | N | N |