| Variant ID: vg1105183882 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr11 | Position: 5183882 |
| Reference Allele: G | Alternative Allele: GTGGAGA,C |
| Primary Allele: G | Secondary Allele: GTGGAGA |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.61, C: 0.39, others allele: 0.00, population size: 41. )
TCACATGGGACTAAATCCCATCCTGACCATAAGATGCGTGACTTCGGTGCAGACTTTTTTCTTTGGGCATGTGATATTACTGATGTTTGGGGTCTTAGGG[G/GTGGAGA,C]
CTGTTTGGTTTCCAGGGACTTATTCCAATTCCATGTCACATCGGATGTTTGGATACTAATTTGGAGTATTAAACATACACTAATTACAAAACACATTCCA
TGGAATGTGTTTTGTAATTAGTGTATGTTTAATACTCCAAATTAGTATCCAAACATCCGATGTGACATGGAATTGGAATAAGTCCCTGGAAACCAAACAG[C/TCTCCAC,G]
CCCTAAGACCCCAAACATCAGTAATATCACATGCCCAAAGAAAAAAGTCTGCACCGAAGTCACGCATCTTATGGTCAGGATGGGATTTAGTCCCATGTGA
| Populations | Population Size | Frequency of G(primary allele) | Frequency of GTGGAGA(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 10.30% | 2.70% | 12.55% | 74.38% | C: 0.06% |
| All Indica | 2759 | 1.20% | 2.00% | 9.17% | 87.50% | C: 0.11% |
| All Japonica | 1512 | 28.30% | 4.00% | 17.92% | 49.74% | NA |
| Aus | 269 | 1.90% | 3.30% | 17.10% | 77.70% | NA |
| Indica I | 595 | 2.50% | 1.00% | 2.35% | 94.12% | NA |
| Indica II | 465 | 0.60% | 0.60% | 3.01% | 95.48% | C: 0.22% |
| Indica III | 913 | 0.80% | 3.70% | 16.98% | 78.53% | NA |
| Indica Intermediate | 786 | 1.10% | 1.50% | 8.91% | 88.17% | C: 0.25% |
| Temperate Japonica | 767 | 33.60% | 3.00% | 20.21% | 43.16% | NA |
| Tropical Japonica | 504 | 14.70% | 6.20% | 11.90% | 67.26% | NA |
| Japonica Intermediate | 241 | 39.80% | 2.90% | 23.24% | 34.02% | NA |
| VI/Aromatic | 96 | 5.20% | 3.10% | 11.46% | 80.21% | NA |
| Intermediate | 90 | 16.70% | 0.00% | 13.33% | 70.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1105183882 | G -> GTGGAGA | LOC_Os11g09710.1 | disruptive_inframe_insertion ; p.Gly319_Cys320insGlyAsp; MODERATE | inframe_variant | Average:19.337; most accessible tissue: Callus, score: 53.099 | N | N | N | N |
| vg1105183882 | G -> DEL | LOC_Os11g09710.1 | N | frameshift_variant | Average:19.337; most accessible tissue: Callus, score: 53.099 | N | N | N | N |
| vg1105183882 | G -> C | LOC_Os11g09710.1 | missense_variant ; p.Gly319Ala; MODERATE | nonsynonymous_codon ; G319A | Average:19.337; most accessible tissue: Callus, score: 53.099 | unknown | unknown | DELETERIOUS | 0.00 |