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Detailed information for vg1023166372:
| Variant ID: vg1023166372 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 23166372 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 331. )
Flanking Sequence (100 bp) in Reference Genome:
TATAGGACATGGGGTAGTCAACACCCAGTCCACCTCTCCCAAGATAAAGGCAAGGTCGAGTTCTCTTTTCCATTCTTCGTAGTTATCTCCTTTCAGGGTC[G/A]
GAATATCTTTAATGTAACCCATCAAGGAGTAGCCACCTGAGATAATCATGTATTGTGAGAACAAAATTAACATTAAAATTATTATGTATTAAGTCTACAT
Reverse complement sequence
ATGTAGACTTAATACATAATAATTTTAATGTTAATTTTGTTCTCACAATACATGATTATCTCAGGTGGCTACTCCTTGATGGGTTACATTAAAGATATTC[C/T]
GACCCTGAAAGGAGATAACTACGAAGAATGGAAAAGAGAACTCGACCTTGCCTTTATCTTGGGAGAGGTGGACTGGGTGTTGACTACCCCATGTCCTATA
Allele Frequencies:
| Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 86.80% | 0.00% | 0.70% | 12.42% | NA |
| All Indica | 2759 | 78.70% | 0.10% | 1.12% | 20.08% | NA |
| All Japonica | 1512 | 99.80% | 0.00% | 0.07% | 0.13% | NA |
| Aus | 269 | 91.40% | 0.00% | 0.37% | 8.18% | NA |
| Indica I | 595 | 60.70% | 0.00% | 2.86% | 36.47% | NA |
| Indica II | 465 | 71.20% | 0.20% | 0.43% | 28.17% | NA |
| Indica III | 913 | 94.50% | 0.00% | 0.33% | 5.15% | NA |
| Indica Intermediate | 786 | 78.50% | 0.10% | 1.15% | 20.23% | NA |
| Temperate Japonica | 767 | 99.90% | 0.00% | 0.00% | 0.13% | NA |
| Tropical Japonica | 504 | 99.60% | 0.00% | 0.20% | 0.20% | NA |
| Japonica Intermediate | 241 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 99.00% | 0.00% | 0.00% | 1.04% | NA |
| Intermediate | 90 | 91.10% | 0.00% | 0.00% | 8.89% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1023166372 | G -> A | LOC_Os10g42980.1 | missense_variant ; p.Pro22Leu; MODERATE | nonsynonymous_codon ; P22L | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | benign  |
0.378 |
TOLERATED | 0.09 |
| vg1023166372 | G -> DEL | LOC_Os10g42980.1 | N | frameshift_variant | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |