Table 1 Statistics for the Nanopore and HiFi genome assemblies of Pt76. Statistics are shown for the clean assemblies with mitochondrial contigs, low-coverage contigs and contaminants removed. Assembly sizes and BUSCO statistics indicate that the two haplotypes are resolved in the HiFi assemblies. SNP calling shows that the HiFi assemblies are a highly accurate representation of the haplotypes, whereas the Nanopore assembly is a pseudo-haplotype representation of the genome
Statistic | Nanopore assembly | HiFi-Canu assembly | HiFi-hifiasm assembly |
|---|---|---|---|
Assembly size | 233.2 Mb | 256.5 Mb | 260.3 Mb |
# of contigs | 717 | 600 | 608 |
Assembly N/L50 | 35/1.1 Mb | 26/2.4 Mb | 24/3.0 Mb |
Assembly N/L90 | 420/115.2 Kb | 124/346.9 Kb | 102/476.9 Kb |
Maximum contig length | 7.8 Mb | 9.3 Mb | 9.4 Mb |
GC content | 46.6% | 46.5% | 46.3% |
% main genome in scaffolds > 50 Kb | 99.4% | 95.8% | 95.0% |
Complete BUSCOs (%) | 95.7% | 96.2% | 96.4% |
Duplicated BUSCOs (%) | 50.4% | 93.1% | 93.1% |
Fragmented BUSCOs (%) | 2.9% | 2.5% | 2.2% |
Missing BUSCOs (%) | 1.4% | 1.3% | 1.4% |
k-mer completeness | 95.8% | 96.4% | 96.4% |
Estimated collapsed regions | 30.9 Mb | 6.4 Mb | 4.7 Mb |
Estimated haploid size | 132.1 Mb | 131.4 Mb | 132.5 Mb |
Illumina SNPs per Mb | 304.0 | 7.1 | 4.3 |
Homozygous SNPs per Mb | 126.5 | 4.1 | 2.9 |
Heterozygous SNPs per Mb | 177.5 | 3.0 | 1.4 |
Illumina SNPs per Mb in collapsed regions | 784.3 | 10.9 | 2.4 |
Homozygous SNPs per Mb in collapsed regions | 89.1 | 4.1 | 0.4 |
Heterozygous SNPs per Mb in collapsed regions | 695.2 | 6.9 | 1.9 |
Illumina SNPs per Mb in non-collapsed regions | 230.6 | 7.0 | 4.3 |
Homozygous SNPs per Mb in non-collapsed regions | 132.2 | 4.1 | 2.9 |
Heterozygous SNPs per Mb in non-collapsed regions | 98.4 | 2.9 | 1.4 |