| Variant ID: vg1012223969 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 12223969 |
| Reference Allele: G | Alternative Allele: C |
| Primary Allele: G | Secondary Allele: C |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.95, C: 0.05, others allele: 0.00, population size: 42. )
GGGAGCGGGTAGCGGCGACCGCGCGCCAGGAGCGACCAATGGCGCGGATGCGGACACGGTCGGGGAGGGAGCGCGAGGACGGCGGCGTGGAGCGTGAGCA[G/C]
GAGGCGGCTGCGCGCAAGGCCGGCAACGGCGGTGCGGAGCGCGAGCAGGATGTGGCCGTGCGCGAGAAGGCTGTTGAACGCTGGCCGGTACGAGGCTTGC
GCAAGCCTCGTACCGGCCAGCGTTCAACAGCCTTCTCGCGCACGGCCACATCCTGCTCGCGCTCCGCACCGCCGTTGCCGGCCTTGCGCGCAGCCGCCTC[C/G]
TGCTCACGCTCCACGCCGCCGTCCTCGCGCTCCCTCCCCGACCGTGTCCGCATCCGCGCCATTGGTCGCTCCTGGCGCGCGGTCGCCGCTACCCGCTCCC
| 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 | 31.60% | 16.00% | 1.90% | 50.53% | NA |
| All Indica | 2759 | 3.30% | 25.80% | 2.72% | 68.14% | NA |
| All Japonica | 1512 | 89.40% | 0.30% | 0.26% | 10.12% | NA |
| Aus | 269 | 1.50% | 9.30% | 1.86% | 87.36% | NA |
| Indica I | 595 | 4.50% | 6.70% | 2.52% | 86.22% | NA |
| Indica II | 465 | 4.10% | 28.80% | 5.59% | 61.51% | NA |
| Indica III | 913 | 1.90% | 32.30% | 1.53% | 64.29% | NA |
| Indica Intermediate | 786 | 3.70% | 30.90% | 2.54% | 62.85% | NA |
| Temperate Japonica | 767 | 97.00% | 0.30% | 0.13% | 2.61% | NA |
| Tropical Japonica | 504 | 81.70% | 0.20% | 0.40% | 17.66% | NA |
| Japonica Intermediate | 241 | 80.90% | 0.40% | 0.41% | 18.26% | NA |
| VI/Aromatic | 96 | 6.20% | 2.10% | 4.17% | 87.50% | NA |
| Intermediate | 90 | 45.60% | 12.20% | 2.22% | 40.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1012223969 | G -> C | LOC_Os10g23830.1 | missense_variant ; p.Gln21His; MODERATE | nonsynonymous_codon ; Q21H | Average:12.655; most accessible tissue: Callus, score: 51.074 | unknown | unknown | TOLERATED | 0.25 |
| vg1012223969 | G -> DEL | LOC_Os10g23830.1 | N | frameshift_variant | Average:12.655; most accessible tissue: Callus, score: 51.074 | N | N | N | N |