Search for Variation information by Variation ID:
Detailed information for vg0100791489:
| Variant ID: vg0100791489 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 791489 |
| Reference Allele: G | Alternative Allele: C |
| Primary Allele: G | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
ACAATCTATCTTTCACTAAAGACAAGATATAATGAAGAGATACATTTGAAGGTCGAAATGTTTCTCAAGACATATGGCACATCGAAACCCACAAGGTATA[G/C]
TTTCTCTGAAGTTAAGAAGATTACAAGACGGTTCAGGGAAAAGATAGGCCACGGTGGGTATGGAAATGTATACAAGGGTGAGCTACCAAATGGAGTGCCC
Reverse complement sequence
GGGCACTCCATTTGGTAGCTCACCCTTGTATACATTTCCATACCCACCGTGGCCTATCTTTTCCCTGAACCGTCTTGTAATCTTCTTAACTTCAGAGAAA[C/G]
TATACCTTGTGGGTTTCGATGTGCCATATGTCTTGAGAAACATTTCGACCTTCAAATGTATCTCTTCATTATATCTTGTCTTTAGTGAAAGATAGATTGT
Allele Frequencies:
| Populations | Population Size | Frequency of G(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 56.40% | 1.10% | 2.14% | 40.35% | NA |
| All Indica | 2759 | 50.30% | 1.40% | 2.46% | 45.85% | NA |
| All Japonica | 1512 | 73.00% | 0.10% | 1.32% | 25.53% | NA |
| Aus | 269 | 36.40% | 5.20% | 1.86% | 56.51% | NA |
| Indica I | 595 | 69.40% | 0.70% | 0.50% | 29.41% | NA |
| Indica II | 465 | 75.90% | 0.00% | 0.86% | 23.23% | NA |
| Indica III | 913 | 18.90% | 3.00% | 2.74% | 75.36% | NA |
| Indica Intermediate | 786 | 57.10% | 0.90% | 4.58% | 37.40% | NA |
| Temperate Japonica | 767 | 70.30% | 0.30% | 1.69% | 27.77% | NA |
| Tropical Japonica | 504 | 83.10% | 0.00% | 0.40% | 16.47% | NA |
| Japonica Intermediate | 241 | 60.60% | 0.00% | 2.07% | 37.34% | NA |
| VI/Aromatic | 96 | 10.40% | 0.00% | 5.21% | 84.38% | NA |
| Intermediate | 90 | 71.10% | 0.00% | 3.33% | 25.56% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0100791489 | G -> DEL | LOC_Os01g02440.1 | N | frameshift_variant | Average:53.024; most accessible tissue: Zhenshan97 panicle, score: 68.538 | N | N | N | N |
| vg0100791489 | G -> C | LOC_Os01g02440.1 | missense_variant ; p.Ser255Thr; MODERATE | nonsynonymous_codon ; S255T | Average:53.024; most accessible tissue: Zhenshan97 panicle, score: 68.538 | benign  |
-0.478 |
TOLERATED | 1.00 |