| Variant ID: vg1225599558 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 25599558 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 272. )
ATGGGTCTCAAACCCATCTCCTTCGATGCATTGTCTATCACATTTCGTGATAGTCCCTTCGTGAAAGGATCTGCCAGGTTTCTCGCTGTTTGGATGTAAT[C/T]
CAACGTTATAACTCCGGAGTTTCTTAATTTCCTGACAGACTTCAATCGTCTTTTCACATGTCTAGACGATTTCATATTATCCTTAGAACTATTCACTTTG
CAAAGTGAATAGTTCTAAGGATAATATGAAATCGTCTAGACATGTGAAAAGACGATTGAAGTCTGTCAGGAAATTAAGAAACTCCGGAGTTATAACGTTG[G/A]
ATTACATCCAAACAGCGAGAAACCTGGCAGATCCTTTCACGAAGGGACTATCACGAAATGTGATAGACAATGCATCGAAGGAGATGGGTTTGAGACCCAT
| 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 | 55.60% | 0.20% | 12.63% | 31.63% | NA |
| All Indica | 2759 | 43.50% | 0.00% | 13.19% | 43.31% | NA |
| All Japonica | 1512 | 86.00% | 0.50% | 13.36% | 0.13% | NA |
| Aus | 269 | 3.00% | 0.00% | 4.09% | 92.94% | NA |
| Indica I | 595 | 86.70% | 0.00% | 2.86% | 10.42% | NA |
| Indica II | 465 | 19.80% | 0.00% | 13.76% | 66.45% | NA |
| Indica III | 913 | 31.00% | 0.00% | 21.25% | 47.75% | NA |
| Indica Intermediate | 786 | 39.30% | 0.00% | 11.32% | 49.36% | NA |
| Temperate Japonica | 767 | 84.60% | 1.00% | 14.34% | 0.00% | NA |
| Tropical Japonica | 504 | 96.00% | 0.00% | 3.97% | 0.00% | NA |
| Japonica Intermediate | 241 | 69.30% | 0.00% | 29.88% | 0.83% | NA |
| VI/Aromatic | 96 | 60.40% | 0.00% | 12.50% | 27.08% | NA |
| Intermediate | 90 | 66.70% | 0.00% | 8.89% | 24.44% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1225599558 | C -> DEL | LOC_Os12g41280.1 | N | frameshift_variant | Average:19.867; most accessible tissue: Zhenshan97 flag leaf, score: 29.417 | N | N | N | N |
| vg1225599558 | C -> T | LOC_Os12g41280.1 | missense_variant ; p.Asp1269Asn; MODERATE | nonsynonymous_codon ; D1269N | Average:19.867; most accessible tissue: Zhenshan97 flag leaf, score: 29.417 | unknown | unknown | DELETERIOUS | 0.01 |