| Variant ID: vg1105974510 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 5974510 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.62, G: 0.37, others allele: 0.00, population size: 76. )
ATCGGCGGCACGGGGCGGTTTCGGCTCGCGCGCGGGTACATGGTCACCAAGAACTACGACTACAGCCTCGCCACCGGCGGCGTCGTCCAGATCGACGTCT[G/A]
CCTGCAGCACTAGCTAGCCATGGACAGAAAACGCACGCGACTGCTGCATATATGCATGGCTGCATCATCTGTGCGAGGAGTTGTGCAGCGGTGGATTCAG
CTGAATCCACCGCTGCACAACTCCTCGCACAGATGATGCAGCCATGCATATATGCAGCAGTCGCGTGCGTTTTCTGTCCATGGCTAGCTAGTGCTGCAGG[C/T]
AGACGTCGATCTGGACGACGCCGCCGGTGGCGAGGCTGTAGTCGTAGTTCTTGGTGACCATGTACCCGCGCGCGAGCCGAAACCGCCCCGTGCCGCCGAT
| 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 | 34.60% | 14.90% | 0.74% | 49.77% | NA |
| All Indica | 2759 | 15.40% | 17.10% | 0.98% | 66.51% | NA |
| All Japonica | 1512 | 68.70% | 13.90% | 0.33% | 17.06% | NA |
| Aus | 269 | 17.10% | 1.90% | 0.74% | 80.30% | NA |
| Indica I | 595 | 35.50% | 1.50% | 0.50% | 62.52% | NA |
| Indica II | 465 | 14.40% | 9.70% | 1.94% | 73.98% | NA |
| Indica III | 913 | 2.60% | 28.00% | 0.44% | 68.89% | NA |
| Indica Intermediate | 786 | 15.80% | 20.50% | 1.40% | 62.34% | NA |
| Temperate Japonica | 767 | 69.20% | 2.60% | 0.52% | 27.64% | NA |
| Tropical Japonica | 504 | 64.90% | 31.50% | 0.20% | 3.37% | NA |
| Japonica Intermediate | 241 | 75.10% | 12.90% | 0.00% | 12.03% | NA |
| VI/Aromatic | 96 | 88.50% | 0.00% | 0.00% | 11.46% | NA |
| Intermediate | 90 | 41.10% | 22.20% | 1.11% | 35.56% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1105974510 | G -> A | LOC_Os11g10840.1 | missense_variant ; p.Cys64Tyr; MODERATE | nonsynonymous_codon ; C64Y | Average:45.682; most accessible tissue: Callus, score: 75.127 | unknown | unknown | TOLERATED | 1.00 |
| vg1105974510 | G -> DEL | LOC_Os11g10840.1 | N | frameshift_variant | Average:45.682; most accessible tissue: Callus, score: 75.127 | N | N | N | N |