| Variant ID: vg0629062080 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 29062080 |
| Reference Allele: G | Alternative Allele: T |
| Primary Allele: G | Secondary Allele: T |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.72, T: 0.29, others allele: 0.00, population size: 295. )
ACGTCTCTGTACCCCAGGGCCAGCAGCATTTGATGATTTCACACCATTGGTAGAATTTCGAGGTATAGTGGACCGATTAACAAAAGCAGAAGCAGTTTGA[G/T]
GTCTAATCTGACACAATTCTTCTTTACCCTTCTGCTGACGTGATTTAGATCTCAAAGCAGCATTTCTGACTACAGAACCAATTGCATGTGCAGACACCCC
GGGGTGTCTGCACATGCAATTGGTTCTGTAGTCAGAAATGCTGCTTTGAGATCTAAATCACGTCAGCAGAAGGGTAAAGAAGAATTGTGTCAGATTAGAC[C/A]
TCAAACTGCTTCTGCTTTTGTTAATCGGTCCACTATACCTCGAAATTCTACCAATGGTGTGAAATCATCAAATGCTGCTGGCCCTGGGGTACAGAGACGT
| Populations | Population Size | Frequency of G(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 75.00% | 24.20% | 0.19% | 0.55% | NA |
| All Indica | 2759 | 65.70% | 33.20% | 0.29% | 0.83% | NA |
| All Japonica | 1512 | 97.80% | 2.10% | 0.00% | 0.13% | NA |
| Aus | 269 | 68.00% | 31.60% | 0.37% | 0.00% | NA |
| Indica I | 595 | 45.00% | 53.40% | 0.17% | 1.34% | NA |
| Indica II | 465 | 61.90% | 37.00% | 0.22% | 0.86% | NA |
| Indica III | 913 | 80.30% | 18.90% | 0.22% | 0.55% | NA |
| Indica Intermediate | 786 | 66.70% | 32.10% | 0.51% | 0.76% | NA |
| Temperate Japonica | 767 | 97.90% | 2.00% | 0.00% | 0.13% | NA |
| Tropical Japonica | 504 | 97.80% | 2.20% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 97.50% | 2.10% | 0.00% | 0.41% | NA |
| VI/Aromatic | 96 | 10.40% | 89.60% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 67.80% | 31.10% | 0.00% | 1.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0629062080 | G -> T | LOC_Os06g48040.1 | missense_variant ; p.Pro188His; MODERATE | nonsynonymous_codon ; P188H | Average:71.9; most accessible tissue: Minghui63 flower, score: 83.608 | unknown | unknown | TOLERATED | 0.60 |
| vg0629062080 | G -> DEL | LOC_Os06g48040.1 | N | frameshift_variant | Average:71.9; most accessible tissue: Minghui63 flower, score: 83.608 | N | N | N | N |