Search for Variation information by Variation ID:
Detailed information for vg0131449624:
| Variant ID: vg0131449624 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 31449624 |
| Reference Allele: T | Alternative Allele: G |
| Primary Allele: T | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
CTGTCCTTTCAGGGCCATGAGAAAGAAATTCGCCATGACCCTGTCGTCACCCCCGGCGGCCTCGATCCCGGTCGTGTAGACCTGGAGAAACTCGGCGGGG[T/G]
TGACGCTCCCGTCATATTTTTCGGCGATGGTGGGCCGGAACCTTGGGGGCCAACGGACATTCCGAAGGCTCGCCACAAAGGCTCTACAGCCGACACCACC
Reverse complement sequence
GGTGGTGTCGGCTGTAGAGCCTTTGTGGCGAGCCTTCGGAATGTCCGTTGGCCCCCAAGGTTCCGGCCCACCATCGCCGAAAAATATGACGGGAGCGTCA[A/C]
CCCCGCCGAGTTTCTCCAGGTCTACACGACCGGGATCGAGGCCGCCGGGGGTGACGACAGGGTCATGGCGAATTTCTTTCTCATGGCCCTGAAAGGACAG
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 | 31.00% | 0.10% | 0.28% | 68.64% | NA |
| All Indica | 2759 | 2.10% | 0.10% | 0.33% | 97.50% | NA |
| All Japonica | 1512 | 82.70% | 0.20% | 0.20% | 16.87% | NA |
| Aus | 269 | 0.70% | 0.00% | 0.00% | 99.26% | NA |
| Indica I | 595 | 3.00% | 0.00% | 0.50% | 96.47% | NA |
| Indica II | 465 | 0.90% | 0.20% | 0.65% | 98.28% | NA |
| Indica III | 913 | 0.40% | 0.00% | 0.11% | 99.45% | NA |
| Indica Intermediate | 786 | 4.10% | 0.10% | 0.25% | 95.55% | NA |
| Temperate Japonica | 767 | 87.10% | 0.30% | 0.39% | 12.26% | NA |
| Tropical Japonica | 504 | 90.30% | 0.00% | 0.00% | 9.72% | NA |
| Japonica Intermediate | 241 | 53.10% | 0.40% | 0.00% | 46.47% | NA |
| VI/Aromatic | 96 | 95.80% | 0.00% | 0.00% | 4.17% | NA |
| Intermediate | 90 | 67.80% | 0.00% | 1.11% | 31.11% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0131449624 | T -> G | LOC_Os01g54660.1 | missense_variant ; p.Asn250Thr; MODERATE | nonsynonymous_codon | Average:23.122; most accessible tissue: Zhenshan97 root, score: 57.64 | possibly damaging  |
1.811 |
DELETERIOUS | 0.00 |
| vg0131449624 | T -> DEL | LOC_Os01g54660.1 | N | frameshift_variant | Average:23.122; most accessible tissue: Zhenshan97 root, score: 57.64 | N | N | N | N |