Additional file 1 of Fine dissection of limber pine resistance to Cronartium ribicola using targeted sequencing of the NLR family
Bibliographic record
Abstract
Additional file 1: Fig. S1. Distribution of minor allele frequency (MAF) of SNP loci detected in limber pine resistant gene analogs (RGAs). Fig. S2. SNP frequencies of limber pine resistance gene analogs (RGAs). Fig. S3. Sequencing depth of SNP loci in individual samples. The percentages of total SNPs (x-axis) have a coverage of a certain depth (y-axis). SNP depth was assessed in each individual of seed family LJ-112. The plot displays data for SNPs (967) with MAF ≥ 0.3 and about 70% of them have a minimum depth at 10 x in all samples except one. Fig. S4. The extent of missing data for 967 SNP loci in 96 individual samples of seed family LJ-112. Individual samples with missing data were calculated as a percentage of the total (y-axis) and plotted across the cumulative total SNPs (x-axis). Over 80% of total SNPs showed missing data in less than 10% of total individual samples. Fig. S5. Correlation of SNP positions of the same NLR gene mapped on the same linkage groups (LGs) by both Fluidigm amplicon-bases targeted-seq (TS) and whole exome-seq (WES). (a) Comparison of TS and WES in seed family LJ-112; (b) comparison of TS and WES between seed families LJ-112 and PHA-106. Fig. S6. Physical distances (bp) of paired SNPs mapped by Fluidigm amplicon-bases targeted-seq (TS) and whole exome-seq (WES). Fig. S7. Identification of NLR alleles significantly associated with MGR-conferred phenotypes using extreme-phenotype genome-wide association study (XP-GWAS). (a) Quantile–quantile plot of the test statistic: 5608 SNPs detected in 354 RGAs with coverage > 50 were subjected to association analysis. (b) Manhattan plot: top SNPs were selected for each genes and plotted against genetic maps of 12 linkage groups, and those genes not mapped so far were included as a separate group. Significant threshold value (p = 1.69 × 10− 4) is presented by a horizontal dash line.
Fetched live from OpenAlex and de-inverted. Abstracts are not stored in this database: the inverted indexes are 8.6 GB of the frame’s 9.3 GB of text, and the host has 13 GB free.
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 | 0.014 |
| Meta-epidemiology (narrow) | 0.001 | 0.001 |
| Meta-epidemiology (broad) | 0.002 | 0.001 |
| Bibliometrics | 0.002 | 0.003 |
| Science and technology studies | 0.001 | 0.000 |
| Scholarly communication | 0.002 | 0.002 |
| Open science | 0.003 | 0.001 |
| Research integrity | 0.002 | 0.001 |
| Insufficient payload (model declined to judge) | 0.835 | 0.165 |
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".