Additional file 3 of De novo assembly of the olive fruit fly (Bactrocera oleae) genome with linked-reads and long-read technologies minimizes gaps and provides exceptional Y chromosome assembly
Bibliographic record
Abstract
Additional file 3: Figure S1. Schematic of the method used to generate the main assembly reported. Figure S2. Genome size and heterozygosity estimation. Figure S3. Contig length at different Nx values for assemblies in Supplementary Table S3. Figure S4. Contiguity plot generated using Quast. Figure S5. Contig length at different Nx values for assemblies in Supplementary Table S4. Figure S6. Plot showing Y chromosome scaffolds/contigs identified in 3 different assemblies (Supplementary Table S4). Figure S7. Total length of scaffolds that were localized to each polytene chromosome and XY chromosomes. Figure S8. Alignment rates of RNA-seq reads from 12 different Bactrocera oleae datasets (see Supplementary Table S9). Figure S9. Complete Basic Universal Single Copy Orthologs (BUSCOs) identified in genome assemblies (Supplementary Table S3). Figure S10. Schematic of the PiRATE pipeline. Figure S11. Histogram of transcripts read lengths. Figure S12. Percentage of Arthropoda Basic Universal Single Copy Orthologs (BUSCOs) captured in 19 arthropod transcriptomes. Figure S13. Number of JAMg predicted B. oleae genes located on the scaffolds assigned to polytene element. Figure S14. Gene ontology (GO) classification of B. oleae JAMg predicted proteins. Figure S15. Detailed orthogroup distribution. Figure S16. Hierarchical clustering of 1100 most variable genes among the 4 metamorphotic stages. Figure S17. Most significantly enriched gene ontology (GO) terms among genes that only peak during development. Figure S18. Contig length at different Nx values for assemblies of selected insects.
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How this classification was reachedexpand
Full frame machine prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. The Gemma side is a direct model label for every work in the frame, read from the title-only record. The Codex side is a classifier learned from the 10,348 direct Codex labels and calibrated to design-weighted sample rates; fields without enough sample support carry no Codex call. Candidate is the union of the two sides; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels.
Distilled classifier scores by category (both heads)
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.002 | 0.008 |
| Meta-epidemiology (narrow) | 0.002 | 0.001 |
| Meta-epidemiology (broad) | 0.002 | 0.002 |
| Bibliometrics | 0.002 | 0.003 |
| Science and technology studies | 0.002 | 0.000 |
| Scholarly communication | 0.002 | 0.002 |
| Open science | 0.003 | 0.002 |
| Research integrity | 0.001 | 0.002 |
| Insufficient payload (model declined to judge) | 0.737 | 0.176 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from itClassification
machine, unvalidatedMachine predicted; a candidate call from one source (direct Gemma or distilled Codex), not a consensus.
How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".