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Detailed information for vg1001933309:
| Variant ID: vg1001933309 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 1933309 |
| Reference Allele: C | Alternative Allele: A |
| Primary Allele: C | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
GGATGGTCCTTTTGGTCGGTCGCTAGCATCTTGAAAAGGTAGCTGTACTCCTCCTGTGATAAACTATTTAGATGAACTGCCTTTGCTGTTCCGAACCTTG[C/A]
AAGATTTTCAATCCTACTTATGATTACCACTTTGCTTCCTCCAGCTGTCATCTGACTTACAGTAGAATAGAAGTTTACCCAATCATTTTCATCTATGTCC
Reverse complement sequence
GGACATAGATGAAAATGATTGGGTAAACTTCTATTCTACTGTAAGTCAGATGACAGCTGGAGGAAGCAAAGTGGTAATCATAAGTAGGATTGAAAATCTT[G/T]
CAAGGTTCGGAACAGCAAAGGCAGTTCATCTAAATAGTTTATCACAGGAGGAGTACAGCTACCTTTTCAAGATGCTAGCGACCGACCAAAAGGACCATCC
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 | 84.70% | 0.30% | 0.57% | 14.47% | NA |
| All Indica | 2759 | 77.70% | 0.40% | 0.80% | 21.02% | NA |
| All Japonica | 1512 | 99.50% | 0.00% | 0.00% | 0.46% | NA |
| Aus | 269 | 65.80% | 0.00% | 1.86% | 32.34% | NA |
| Indica I | 595 | 60.70% | 0.50% | 1.34% | 37.48% | NA |
| Indica II | 465 | 85.60% | 0.00% | 0.22% | 14.19% | NA |
| Indica III | 913 | 80.60% | 0.10% | 0.55% | 18.73% | NA |
| Indica Intermediate | 786 | 82.70% | 1.00% | 1.02% | 15.27% | 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 | 93.30% | 0.00% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg1001933309 | C -> A | LOC_Os10g04160.1 | missense_variant ; p.Ala192Ser; MODERATE | nonsynonymous_codon ; A192S | Average:40.867; most accessible tissue: Callus, score: 77.054 | benign  |
1.31 |
TOLERATED | 0.30 |
| vg1001933309 | C -> DEL | LOC_Os10g04160.1 | N | frameshift_variant | Average:40.867; most accessible tissue: Callus, score: 77.054 | N | N | N | N |