Table 3.
Different measures for evaluating the assembly quality of individual genomes. The following introductions of the measures are adapted from the definitions in QUAST [40].
| Measures | Introductions | |
|---|---|---|
| Integrity | Genome fraction | The proportion of the aligned bases in the reference. |
| Duplication ratio | The total bases of the alignment in the assembly divided by the total bases of the alignment in the reference. | |
| Contiguity | N50 | The contig length for which 50% of the bases of the assembly are represented in longer or equal length contigs. |
| NGx | The contig length for which x% of the bases of the reference genome are represented in longer or equal length contigs. | |
| NGAx | NGAx is NGx where the contig lengths are replaced with the lengths of aligned blocks. | |
| L50 | The number of contigs of length at least N50. | |
| LGx | The number of contigs of length at least NGx. | |
| LGAx | LGAx is LGx where the contig lengths are replaced with the lengths of aligned blocks. | |
| Largest alignment | The total bases of the largest continuous alignment in the assembly. | |
| Total aligned length | The total bases of alignment in the assembly. | |
| Accuracy | # misassemblies | The number of misassemblies. |
| Misassembled contig length | The number of total bases contained in all contigs with one or more misassemblies. | |
| # mismatches | The number of mismatches in the alignment. | |
| # indels | The number of indels in the alignment. | |
| Indels length | The number of total bases that indels contain. | |
| # mismatches per 100 kbp | The average number of mismatches per 100 kbp (aligned bases). | |
| # indels per 100 kbp | The average number of indels per 100 kbp (aligned bases). |