| Variant ID: vg0106165875 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 6165875 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.01, others allele: 0.00, population size: 272. )
AACAATGAGATGTCAGCACAAACATGTACATTGGCCCCAGTATCAACCCACCAATTAGTAGATTGATTAACTGAAAAAACAGTAGGTAAATTACCATACC[C/T]
GCTTCCATCTCCAGTGTTGCCAATGGTCACATTAGCAGACTTAGAAGTCTGCCCTGCAGGTGCCTTCATCCCCTTGCGCTGTGGACACTTCCTAGCCAGA
TCTGGCTAGGAAGTGTCCACAGCGCAAGGGGATGAAGGCACCTGCAGGGCAGACTTCTAAGTCTGCTAATGTGACCATTGGCAACACTGGAGATGGAAGC[G/A]
GGTATGGTAATTTACCTACTGTTTTTTCAGTTAATCAATCTACTAATTGGTGGGTTGATACTGGGGCCAATGTACATGTTTGTGCTGACATCTCATTGTT
| Populations | Population Size | Frequency of C(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 0.70% | 0.10% | 2.75% | 96.47% | NA |
| All Indica | 2759 | 0.70% | 0.00% | 2.79% | 96.56% | NA |
| All Japonica | 1512 | 0.50% | 0.00% | 1.65% | 97.88% | NA |
| Aus | 269 | 0.70% | 1.90% | 8.55% | 88.85% | NA |
| Indica I | 595 | 0.30% | 0.00% | 0.17% | 99.50% | NA |
| Indica II | 465 | 0.20% | 0.00% | 3.01% | 96.77% | NA |
| Indica III | 913 | 0.40% | 0.00% | 3.83% | 95.73% | NA |
| Indica Intermediate | 786 | 1.40% | 0.00% | 3.44% | 95.17% | NA |
| Temperate Japonica | 767 | 0.50% | 0.00% | 0.39% | 99.09% | NA |
| Tropical Japonica | 504 | 0.60% | 0.00% | 4.37% | 95.04% | NA |
| Japonica Intermediate | 241 | 0.00% | 0.00% | 0.00% | 100.00% | NA |
| VI/Aromatic | 96 | 0.00% | 0.00% | 3.12% | 96.88% | NA |
| Intermediate | 90 | 5.60% | 0.00% | 2.22% | 92.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0106165875 | C -> T | LOC_Os01g11450.1 | missense_variant ; p.Gly171Arg; MODERATE | nonsynonymous_codon ; G171R | Average:7.658; most accessible tissue: Minghui63 flag leaf, score: 13.491 | unknown | unknown | TOLERATED | 0.11 |
| vg0106165875 | C -> DEL | LOC_Os01g11450.1 | N | frameshift_variant | Average:7.658; most accessible tissue: Minghui63 flag leaf, score: 13.491 | N | N | N | N |