| Variant ID: vg1113567937 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr11 | Position: 13567937 |
| Reference Allele: TGGCGCCAACACCGATGCCCCATCAATTGGCTAACTCGTCAGTCTGTTACCC | Alternative Allele: T |
| Primary Allele: TGGCGCCAACACCGATGCCC CATCAATTGGCTAACTCGTC AGTCTGTTACCC | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
CCAGTCAAAATAAAAAAGTTTGACCAGGCCTTGTGCGACCTTGGAGCCAGTGTCAGCGTCATGCCAAAAGACGTCTTCGACAAGCTCAACTTCACGGTGT[TGGCGCCAACACCGATGCCCCATCAATTGGCTAACTCGTCAGTCTGTTACCC/T]
GGCAGAGATAGCGGAGGATGTGCCAGTCAAGATACGGGATTTCTTCATCCCGGTTGACTTTGTGGTGCTGGACATGGACATAGGAAAAGAGACGCCGCTC
GAGCGGCGTCTCTTTTCCTATGTCCATGTCCAGCACCACAAAGTCAACCGGGATGAAGAAATCCCGTATCTTGACTGGCACATCCTCCGCTATCTCTGCC[GGGTAACAGACTGACGAGTTAGCCAATTGATGGGGCATCGGTGTTGGCGCCA/A]
ACACCGTGAAGTTGAGCTTGTCGAAGACGTCTTTTGGCATGACGCTGACACTGGCTCCAAGGTCGCACAAGGCCTGGTCAAACTTTTTTATTTTGACTGG
| Populations | Population Size | Frequency of TGGCGCCAACACCGATGCCC CATCAATTGGCTAACTCGTC AGTCTGTTACCC(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 76.20% | 23.70% | 0.15% | 0.00% | NA |
| All Indica | 2759 | 69.20% | 30.60% | 0.25% | 0.00% | NA |
| All Japonica | 1512 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| Aus | 269 | 12.60% | 87.40% | 0.00% | 0.00% | NA |
| Indica I | 595 | 91.10% | 8.90% | 0.00% | 0.00% | NA |
| Indica II | 465 | 43.00% | 56.30% | 0.65% | 0.00% | NA |
| Indica III | 913 | 72.20% | 27.60% | 0.22% | 0.00% | NA |
| Indica Intermediate | 786 | 64.60% | 35.10% | 0.25% | 0.00% | NA |
| Temperate Japonica | 767 | 99.70% | 0.30% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 99.40% | 0.60% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 90.60% | 9.40% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 72.20% | 27.80% | 0.00% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1113567937 | TGGCGCCAACACCGATGCCCCATCAATTGGCTAACTCGTCAGTCTGTTACCC -> T | LOC_Os11g23950.1 | disruptive_inframe_deletion ; p.Pro16_Ala32del; MODERATE | inframe_variant | Average:32.581; most accessible tissue: Minghui63 flag leaf, score: 45.195 | N | N | N | N |