Search for Variation information by Variation ID:
Detailed information for vg1001933049:
| Variant ID: vg1001933049 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 1933049 |
| Reference Allele: T | Alternative Allele: G |
| Primary Allele: T | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
GCTTTACAAGAATGCAGGCGTGAGTAGGATAAGATGTCATAAATTCGGTGCTATCTACTGGCTGCTCTTTCTCAATGATATCTTTCGGATGCTCACCATA[T/G]
TTCAAAAAGTTGTTCTTCACCATCCTCTCGAAGCGTCGCAATATTCTAAGCCAGAAGTGAACATTATGGTTCCTTCTAAGCATGTCAGATATCATATTGG
Reverse complement sequence
CCAATATGATATCTGACATGCTTAGAAGGAACCATAATGTTCACTTCTGGCTTAGAATATTGCGACGCTTCGAGAGGATGGTGAAGAACAACTTTTTGAA[A/C]
TATGGTGAGCATCCGAAAGATATCATTGAGAAAGAGCAGCCAGTAGATAGCACCGAATTTATGACATCTTATCCTACTCACGCCTGCATTCTTGTAAAGC
Allele Frequencies:
| Populations | Population Size | Frequency of T(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 80.10% | 4.20% | 0.44% | 15.23% | NA |
| All Indica | 2759 | 70.60% | 6.70% | 0.65% | 22.07% | NA |
| All Japonica | 1512 | 99.00% | 0.50% | 0.00% | 0.46% | NA |
| Aus | 269 | 63.90% | 0.00% | 1.12% | 34.94% | NA |
| Indica I | 595 | 59.50% | 0.20% | 1.34% | 38.99% | NA |
| Indica II | 465 | 73.80% | 11.00% | 0.22% | 15.05% | NA |
| Indica III | 913 | 70.30% | 9.70% | 0.33% | 19.61% | NA |
| Indica Intermediate | 786 | 77.40% | 5.60% | 0.76% | 16.28% | NA |
| Temperate Japonica | 767 | 99.20% | 0.10% | 0.00% | 0.65% | NA |
| Tropical Japonica | 504 | 98.60% | 1.40% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 99.20% | 0.00% | 0.00% | 0.83% | NA |
| VI/Aromatic | 96 | 93.80% | 2.10% | 0.00% | 4.17% | NA |
| Intermediate | 90 | 88.90% | 4.40% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg1001933049 | T -> G | LOC_Os10g04160.1 | missense_variant ; p.Lys278Asn; MODERATE | nonsynonymous_codon ; K278N | Average:37.805; most accessible tissue: Callus, score: 73.936 | possibly damaging  |
1.785 |
TOLERATED | 0.51 |
| vg1001933049 | T -> DEL | LOC_Os10g04160.1 | N | frameshift_variant | Average:37.805; most accessible tissue: Callus, score: 73.936 | N | N | N | N |