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Detailed information for vg1021203566:
| Variant ID: vg1021203566 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 21203566 |
| Reference Allele: G | Alternative Allele: C |
| Primary Allele: G | Secondary Allele: C |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 304. )
Flanking Sequence (100 bp) in Reference Genome:
TCAAATACATATATATCCTTGATGGTTAACCTTGTTTACAATGTAAAATACAAAACAGGTACCTTCTTATGTGATGCTTGGAGTTCCAAAGCCTGAAGAA[G/C]
TACCAAAGGCGCCTCCCGCCCCACAGCACCCACTTTCTCCCATGGGAGAGGCCTGTTCCAGGATGGACCTTACTGCCATCCATCAGATCCTAGTTTCAAC
Reverse complement sequence
GTTGAAACTAGGATCTGATGGATGGCAGTAAGGTCCATCCTGGAACAGGCCTCTCCCATGGGAGAAAGTGGGTGCTGTGGGGCGGGAGGCGCCTTTGGTA[C/G]
TTCTTCAGGCTTTGGAACTCCAAGCATCACATAAGAAGGTACCTGTTTTGTATTTTACATTGTAAACAAGGTTAACCATCAAGGATATATATGTATTTGA
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 | 99.70% | 0.20% | 0.06% | 0.00% | NA |
| All Indica | 2759 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 99.10% | 0.70% | 0.20% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica III | 913 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 99.90% | 0.00% | 0.13% | 0.00% | NA |
| Tropical Japonica | 504 | 99.00% | 1.00% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 97.10% | 2.10% | 0.83% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1021203566 | G -> C | LOC_Os10g39670.1 | missense_variant ; p.Val357Leu; MODERATE | nonsynonymous_codon ; V357L | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | benign  |
-0.05 |
TOLERATED | 0.84 |