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Detailed information for vg1023166388:
| Variant ID: vg1023166388 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 23166388 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 350. )
Flanking Sequence (100 bp) in Reference Genome:
GTCAACACCCAGTCCACCTCTCCCAAGATAAAGGCAAGGTCGAGTTCTCTTTTCCATTCTTCGTAGTTATCTCCTTTCAGGGTCGGAATATCTTTAATGT[A/G]
ACCCATCAAGGAGTAGCCACCTGAGATAATCATGTATTGTGAGAACAAAATTAACATTAAAATTATTATGTATTAAGTCTACATCACCGTTGGGCAGAAA
Reverse complement sequence
TTTCTGCCCAACGGTGATGTAGACTTAATACATAATAATTTTAATGTTAATTTTGTTCTCACAATACATGATTATCTCAGGTGGCTACTCCTTGATGGGT[T/C]
ACATTAAAGATATTCCGACCCTGAAAGGAGATAACTACGAAGAATGGAAAAGAGAACTCGACCTTGCCTTTATCTTGGGAGAGGTGGACTGGGTGTTGAC
Allele Frequencies:
| Populations | Population Size | Frequency of A(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 84.60% | 1.40% | 1.63% | 12.40% | NA |
| All Indica | 2759 | 76.60% | 1.50% | 1.81% | 20.04% | NA |
| All Japonica | 1512 | 99.70% | 0.10% | 0.13% | 0.13% | NA |
| Aus | 269 | 74.70% | 7.80% | 9.29% | 8.18% | NA |
| Indica I | 595 | 60.70% | 0.00% | 2.86% | 36.47% | NA |
| Indica II | 465 | 67.50% | 2.80% | 1.51% | 28.17% | NA |
| Indica III | 913 | 93.20% | 1.10% | 0.55% | 5.15% | NA |
| Indica Intermediate | 786 | 74.80% | 2.40% | 2.67% | 20.10% | NA |
| Temperate Japonica | 767 | 99.70% | 0.10% | 0.00% | 0.13% | NA |
| Tropical Japonica | 504 | 99.40% | 0.00% | 0.40% | 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 | 90.00% | 1.10% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg1023166388 | A -> G | LOC_Os10g42980.1 | missense_variant ; p.Tyr17His; MODERATE | nonsynonymous_codon ; Y17H | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | probably damaging  |
2.085 |
TOLERATED | 0.27 |
| vg1023166388 | A -> DEL | LOC_Os10g42980.1 | N | frameshift_variant | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |