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Table 2 Proportion of false-positive Hi-C contacts between haplotypes in the assemblies. Only Hi-C reads with high mapping quality (MAPQ > 30) were used in this analysis. Over half of all trans Hi-C contacts in the Nanopore assembly are false-positive signals between haplotypes. In contrast, the HiFi assemblies have a low false-positive signal similarly to the Pgt assembly with phase switches present

From: Physical separation of haplotypes in dikaryons allows benchmarking of phasing accuracy in Nanopore and HiFi assemblies with Hi-C data

Assembly

# of Hi-C cis-contacts

# of Hi-C trans-contacts

False-positive rate of Hi-C contacts (% of Hi-C trans-contacts that are between haplotypes)

Nanopore assembly

634,712

257,489

58.8%

Nanopore assembly (without collapsed regions)

497,011

175,295

62.5%

Nanopore assembly (only collapsed regions)

137,700

82,202

50.9%

Nanopore unpolished assembly

288,065

181,198

52.3%

Nanopore unpolished assembly (without collapsed regions)

212,923

104,190

55.6%

Nanopore unpolished assembly (only collapsed regions)

75,142

77,008

47.8%

HiFi-Canu assembly

304,860

56,033

8.6%

HiFi-Canu assembly (without collapsed regions)

297,661

52,445

7.7%

HiFi-Canu assembly (only collapsed regions)

7198

3587

21.3%

HiFi- hifiasm assembly

305,160

54,850

7.3%

HiFi- hifiasm assembly (without collapsed regions)

299,193

52,350

7.1%

HiFi- hifiasm assembly (only collapsed regions)

5967

2,500

12.2%

Puccinia graminis 21-0 assembly (with phase switches)

1,448,429

75,836

6.4%

Puccinia graminis 21-0 assembly (without phase switches)

1,315,483

65,565

2.7%