Table 2. Mapping statistics for reference-based assembly of Illumina and Nanopore data.
| Illumina (L. virgatum) | Illumina (Artemisia) | Nanopore (L.virgatum) | Nanopore (Artemisia) | |
|---|---|---|---|---|
| input reads (after splitting) | 248,456 | 248,456 | 12,404 (39,080) | 12,404 (39,080) |
| mapped reads (%) | 238,574 (96.02) | 237,686 (95.67) | 38,377 (98.20) | 38,363 (98.17) |
| ambiguously mapped (%) | 36,641 (14.75) | 35,934 (14.46) | 2,341 (5.99) | 2,325 (5.95) |
| read lengths | 50–300 bp | 50–300 bp | 1–3,000 bp | 1–3,000 bp |
| mean coverage (stdev) | 143.41x (88.36) | 143.43x (87.92) | 754.34x (473.68) | 756.68x (472.80) |
| fraction of reference at coverage x or higher | 30x: 99.74% 20x: 99.88% | 30x: 99.66% 20x: 99.81% | 100x: 99.72% 50x: 99.76% | 100x: 99.72% 50x: 99.76% |
| mean mapping quality | 36.5 | 33.4 | 22.4 | 19.6 |
| duplicate reads removed | 7,644 | 7,646 | n.a. | n.a. |
| remaining reads after deduplication (%) | 230,930 (96.8) | 230,040 (96.8) | n.a. | n.a. |
The respective reference used for mapping (the L. virgatum Illumina de novo assembly or A. frigida as obtained from Genbank, both without the IRA) is given in parentheses. Nanopore input reads are given before and after splitting by mapPacBio.sh into 3,000-bp chunks. Mapped reads include ambiguously mapped reads. The percentages given for both refer to all input reads, the fraction of remaining reads after deduplication is relative to mapped reads. No deduplication was performed for Nanopore reads.
L., Leucanthemum; stdev, standard deviation; n.a., not applicable.