Table 3.
Overview of the number of read pairs, mean coverage depth, contig number, contig length and other assembly and contig statistics. Only paired reads were counted for read statistics; orphaned reads were discarded prior to quality filtering. Contig statistics are based on contigs of a size equal to or greater than 1000 bp. Information in square brackets indicates the unit that the values are presented in. Abbreviations: N = number; P = percentage.
| C. aquatica | C. caroliniana cv. ‘Silvergreen’ | C. furcata | |
|---|---|---|---|
| N of read pairs after quality filtering | 1,896,979 | 4,005,075 | 4,132,180 |
| N of read pairs that mapped to the reference genomes (P of quality-filtered pairs) 1 | 73,452 (3.87%) | 55,254 (1.37%) | 46,681 (1.12%) |
| Mean read length [bp] 2,3 | 593.58 | 595.09 | 594.30 |
| Mean coverage depth [fold] 3 | 349.36 | 266.01 | 224.87 |
| P of bases with coverage depth greater than 20-fold, 50-fold, and 100-fold | 99.89%—99.70%—98.51% | 99.97%—99.93%—90.40% | 99.87%—99.76%—89.72% |
| N of contigs after automatic assembly | 3 | 4 | 3 |
| Size of largest contig [bp] | 89,168 | 80,536 | 90,298 |
| Total length of contigs [bp] | 134,685 | 135,444 | 135,367 |
| N50 [bp] | 89,168 | 80,536 | 90,298 |
| L50 | 1 | 1 | 1 |
1 All quality filtered reads that mapped concordantly one or more times to the complete plastid genomes of Cabomba caroliniana and Brasenia schreberi were counted. Read pairs located in the IR usually map to a reference genome more than one time. 2 Calculated as mean length of (R1 plus R2). 3 Calculated from all quality-filtered reads that mapped to the final assembly.