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Detailed information for vg1001933710:
| Variant ID: vg1001933710 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 1933710 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
GTTACCTGGATTTTGCAATAAAAAATTGATAATTTCCTGCTTCTCGACATGATGAGCAAACACACAATTATCGGTGTAAAGGTAAGCATCATAGGGTCGG[C/T]
GACACATGCATTCACATCTGGCTAGGAATACAACAAACTCTTTCACTCTACCTCCATCTGAAGTATTTATGTGTTTTTTGTGCAGCTCTCTAAAAAGCTT
Reverse complement sequence
AAGCTTTTTAGAGAGCTGCACAAAAAACACATAAATACTTCAGATGGAGGTAGAGTGAAAGAGTTTGTTGTATTCCTAGCCAGATGTGAATGCATGTGTC[G/A]
CCGACCCTATGATGCTTACCTTTACACCGATAATTGTGTGTTTGCTCATCATGTCGAGAAGCAGGAAATTATCAATTTTTTATTGCAAAATCCAGGTAAC
Allele Frequencies:
| Populations | Population Size | Frequency of C(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 81.40% | 3.40% | 0.44% | 14.77% | NA |
| All Indica | 2759 | 72.40% | 5.60% | 0.58% | 21.46% | NA |
| All Japonica | 1512 | 99.50% | 0.00% | 0.00% | 0.46% | NA |
| Aus | 269 | 65.10% | 0.00% | 1.86% | 33.09% | NA |
| Indica I | 595 | 60.50% | 0.00% | 1.18% | 38.32% | NA |
| Indica II | 465 | 81.30% | 3.40% | 0.86% | 14.41% | NA |
| Indica III | 913 | 70.90% | 10.10% | 0.11% | 18.95% | NA |
| Indica Intermediate | 786 | 77.90% | 5.90% | 0.51% | 15.78% | NA |
| Temperate Japonica | 767 | 99.30% | 0.00% | 0.00% | 0.65% | NA |
| Tropical Japonica | 504 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 99.20% | 0.00% | 0.00% | 0.83% | NA |
| VI/Aromatic | 96 | 95.80% | 0.00% | 0.00% | 4.17% | NA |
| Intermediate | 90 | 85.60% | 7.80% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg1001933710 | C -> T | LOC_Os10g04160.1 | missense_variant ; p.Arg58His; MODERATE | nonsynonymous_codon ; R58H | Average:39.885; most accessible tissue: Minghui63 root, score: 74.461 | benign  |
0.672 |
TOLERATED | 0.10 |
| vg1001933710 | C -> DEL | LOC_Os10g04160.1 | N | frameshift_variant | Average:39.885; most accessible tissue: Minghui63 root, score: 74.461 | N | N | N | N |