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. 2022 Mar 24;11:giac028. doi: 10.1093/gigascience/giac028

Table 2:

Assembly quality assessment of Cassava TME204 haplotigs generated by hifiasm v0.15.3

Quality Category Quality Metric Haplotype 1 Haplotype 2
General Contig Size (Mb) 762 706
Continuity Contig N50 (Mb) 18 26
Contig NG50 (Mb) 18 22
Largest contig (Mb) 41 44
Base accuracy QV a 45.23 48.94
k-mer completeness (%)a 79.6 79.1
Structural accuracy k-mer false duplications (%)a 3.0 2.4
BUSCO duplicate (%) 4.9 4.2
Reference asmgene duplicate (%) 1.6 0.8
Reference gene transfer duplicate (%)b 3.8 3.2
Reliable blocks (%) 97.2 97.5
Congruent genetic markers (%) 99.8 99.9
Functional completeness BUSCO complete (%) 99.0 98.8
Reference asmgene complete (%) 95.2 95.4
Reference gene transfer rate (%)b 96.3 96.5
Transcript alignment rate (%) 99.3 99.4
a

QV and k-mer completeness for the combined assembly is 46.63 and 98.4%, respectively. The k-mer false duplication rate for the combined assembly is 3.5%.

b

Calculated on the basis of the number of lifted genes regardless of completeness.