TABLE 1.
Summary of recovery statistics produced by HybPiper comparing the default353 target set to the mega353 target set (filtered by family or order). Values represent averages of each data set for each target file.
| Data set (no. of samples) | Target file | % reads on target (average) | No. of loci with sequences (average) | No. of loci at 75% of target length (average) | Length of concatenated loci (bp, average) |
|---|---|---|---|---|---|
| Angiosperms353 exemplar data (41) | default353 | 22.3% | 275.5 | 117.7 | 144,283.5 |
| mega353 | 32.3% | 287.9 | 132.2 | 165,867.4 | |
| mega353 vs. default353 % improvement | 44.9% | 4.5% | 12.3% | 15% | |
| Asparagales (8) | default353 | 1.2% | 146.9 | 22.9 | 55,484.3 |
| Order (Asparagales) | 1.7% | 159.5 | 27.8 | 65,637.4 | |
| Order vs. default353 % improvement | 37.1% | 8.6% | 21.3% | 18.3% | |
| Azorella (5) | default353 | 15.7% | 292.8 | 89 | 131,292.6 |
| Family (Apiaceae) | 16.3% | 299.2 | 107.6 | 144,951 | |
| Order (Apiales) | 19.4% | 309 | 119.8 | 158,014.8 | |
| Family vs. default353 % improvement | 3.7% | 2.2% | 20.9% | 10.4% | |
| Order vs. default353 % improvement | 23.1% | 5.5% | 34.6% | 20.4% | |
| Bulbophyllum (12) | default353 | 12.30% | 238.8 | 46 | 93,043 |
| Family (Orchidaceae) | 14.6% | 268.2 | 75.5 | 122,451.8 | |
| Family + genus (Orchidaceae+Bulbophyllum) | 15% | 273.1 | 83.8 | 131,549.8 | |
| Family vs. default353 % improvement | 19% | 12.3% | 64.1% | 31.6% | |
| Family+genus vs. default353 % improvement | 22.2% | 14.3% | 82.2% | 41.4% | |
| Cyperaceae (6) | default353 | 9.4% | 201.1667 | 68 | 91,865.5 |
| Family (Cyperaceae) | 11.1% | 249 | 103.8333 | 129,220 | |
| Order (Poales) | 12.1% | 251.3333 | 100.3333 | 131,571 | |
| Family vs. default353 % improvement | 18.1% | 23.8% | 52.7% | 40.7% | |
| Order vs. default353 % improvement | 28.3% | 24.9% | 47.5% | 43.2% | |
| Ericaceae (12) | default353 | 7.5% | 307 | 97.2 | 145,031.8 |
| Family (Ericaceae) | 11.9% | 335.8 | 185.6 | 198,784.3 | |
| Order (Ericales) | 12.9% | 338.6 | 189.2 | 205,629 | |
| Family vs. default353 % improvement | 60% | 9.4% | 91% | 37.1% | |
| Order vs. default353 % improvement | 73.3% | 10.3% | 94.7% | 41.8% | |
| Nepenthes (8) | default353 | 8.8% | 306.6 | 105.5 | 145,598.6 |
| Order (Caryophyllales) | 12% | 322.9 | 147.5 | 182,845.1 | |
| Order vs. default353 % improvement | 36% | 5.3% | 39.78% | 25.6% | |
| Sapindales (6) | default353 | 26.6% | 335.6 | 188.6 | 193,205.6 |
| Order (Sapindales) | 31.3% | 341.4 | 248.7 | 229,415.1 | |
| Order vs. default353 % improvement | 17.4% | 1.7% | 31.9% | 18.7% | |
| Average percentage improvement | 31.9% | 10.2% | 49.4% | 28.7% | |
| Minimum percentage improvement | 3.7% | 1.7% | 12.3% | 10.4% | |
| Maximum percentage improvement | 73.3% | 24.9% | 94.7% | 43.2% |