| Variant ID: vg1105183881 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr11 | Position: 5183881 |
| Reference Allele: G | Alternative Allele: GAGTA,T,A |
| Primary Allele: G | Secondary Allele: GAGTA |
Inferred Ancestral Allele: Not determined.
TTCACATGGGACTAAATCCCATCCTGACCATAAGATGCGTGACTTCGGTGCAGACTTTTTTCTTTGGGCATGTGATATTACTGATGTTTGGGGTCTTAGG[G/GAGTA,T,A]
GCTGTTTGGTTTCCAGGGACTTATTCCAATTCCATGTCACATCGGATGTTTGGATACTAATTTGGAGTATTAAACATACACTAATTACAAAACACATTCC
GGAATGTGTTTTGTAATTAGTGTATGTTTAATACTCCAAATTAGTATCCAAACATCCGATGTGACATGGAATTGGAATAAGTCCCTGGAAACCAAACAGC[C/TACTC,A,T]
CCTAAGACCCCAAACATCAGTAATATCACATGCCCAAAGAAAAAAGTCTGCACCGAAGTCACGCATCTTATGGTCAGGATGGGATTTAGTCCCATGTGAA
| Populations | Population Size | Frequency of G(primary allele) | Frequency of GAGTA(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 10.30% | 2.10% | 16.42% | 68.13% | A: 1.74%; T: 1.25% |
| All Indica | 2759 | 1.20% | 1.60% | 14.10% | 79.92% | A: 1.78%; T: 1.34% |
| All Japonica | 1512 | 28.40% | 3.00% | 19.11% | 46.69% | A: 1.59%; T: 1.26% |
| Aus | 269 | 1.90% | 3.70% | 24.91% | 66.54% | A: 1.86%; T: 1.12% |
| Indica I | 595 | 2.40% | 0.20% | 3.36% | 93.45% | A: 0.50%; T: 0.17% |
| Indica II | 465 | 0.60% | 0.60% | 6.02% | 92.04% | A: 0.43%; T: 0.22% |
| Indica III | 913 | 0.90% | 3.30% | 24.10% | 67.47% | A: 2.30%; T: 1.97% |
| Indica Intermediate | 786 | 1.10% | 1.40% | 15.39% | 76.97% | A: 2.93%; T: 2.16% |
| Temperate Japonica | 767 | 33.80% | 2.20% | 21.64% | 40.29% | T: 1.04%; A: 1.04% |
| Tropical Japonica | 504 | 14.70% | 4.60% | 13.29% | 63.29% | A: 2.18%; T: 1.98% |
| Japonica Intermediate | 241 | 39.80% | 2.10% | 23.24% | 32.37% | A: 2.07%; T: 0.41% |
| VI/Aromatic | 96 | 5.20% | 1.00% | 12.50% | 78.12% | A: 3.12% |
| Intermediate | 90 | 16.70% | 0.00% | 21.11% | 61.11% | A: 1.11% |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1105183881 | G -> A | LOC_Os11g09710.1 | missense_variant ; p.Gly319Ser; MODERATE | nonsynonymous_codon ; G319S | Average:19.337; most accessible tissue: Callus, score: 53.099 | unknown | unknown | DELETERIOUS | 0.00 |
| vg1105183881 | G -> T | LOC_Os11g09710.1 | missense_variant ; p.Gly319Cys; MODERATE | nonsynonymous_codon ; G319C | Average:19.337; most accessible tissue: Callus, score: 53.099 | unknown | unknown | DELETERIOUS | 0.00 |
| vg1105183881 | G -> GAGTA | LOC_Os11g09710.1 | frameshift_variant&stop_gained ; p.Gly319fs; HIGH | frameshift_variant | Average:19.337; most accessible tissue: Callus, score: 53.099 | N | N | N | N |
| vg1105183881 | G -> DEL | LOC_Os11g09710.1 | N | frameshift_variant | Average:19.337; most accessible tissue: Callus, score: 53.099 | N | N | N | N |