| Variant ID: vg0826584621 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 26584621 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 105. )
GATGTACCTGGCTAGTGCAACTAGGCCTGATATCTCCTTTGCTGTGAGCAAGTTGAGCCGATTTACCTCTAATCCGGGAGATGATCACTGGCGTGCACTT[G/A]
AGCGAGTAATGCGCTATCTGAAAGGTACTGTGGAATTGGGGCTTCACTATACTGGGTATCCTGCGGTACTGGAGGGTTATAGTGATTCTAACTGGATCTC
GAGATCCAGTTAGAATCACTATAACCCTCCAGTACCGCAGGATACCCAGTATAGTGAAGCCCCAATTCCACAGTACCTTTCAGATAGCGCATTACTCGCT[C/T]
AAGTGCACGCCAGTGATCATCTCCCGGATTAGAGGTAAATCGGCTCAACTTGCTCACAGCAAAGGAGATATCAGGCCTAGTTGCACTAGCCAGGTACATC
| 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 | 17.90% | 0.80% | 25.71% | 55.59% | NA |
| All Indica | 2759 | 7.80% | 1.30% | 31.57% | 59.33% | NA |
| All Japonica | 1512 | 33.50% | 0.00% | 13.69% | 52.84% | NA |
| Aus | 269 | 14.50% | 0.00% | 33.83% | 51.67% | NA |
| Indica I | 595 | 9.20% | 0.30% | 15.63% | 74.79% | NA |
| Indica II | 465 | 5.40% | 0.20% | 26.24% | 68.17% | NA |
| Indica III | 913 | 7.70% | 2.50% | 47.86% | 41.95% | NA |
| Indica Intermediate | 786 | 8.10% | 1.40% | 27.86% | 62.60% | NA |
| Temperate Japonica | 767 | 30.20% | 0.00% | 9.91% | 59.84% | NA |
| Tropical Japonica | 504 | 40.90% | 0.00% | 20.04% | 39.09% | NA |
| Japonica Intermediate | 241 | 28.20% | 0.00% | 12.45% | 59.34% | NA |
| VI/Aromatic | 96 | 70.80% | 0.00% | 20.83% | 8.33% | NA |
| Intermediate | 90 | 21.10% | 1.10% | 28.89% | 48.89% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0826584621 | G -> A | LOC_Os08g42090.1 | missense_variant ; p.Glu1122Lys; MODERATE | nonsynonymous_codon ; E1122K | Average:10.454; most accessible tissue: Minghui63 panicle, score: 20.733 | unknown | unknown | DELETERIOUS | 0.03 |
| vg0826584621 | G -> DEL | LOC_Os08g42090.1 | N | frameshift_variant | Average:10.454; most accessible tissue: Minghui63 panicle, score: 20.733 | N | N | N | N |