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Table 2 Comparison between the resulting switch error rates of WHATSHAP POLYPHASE (WH-PP) and H-POPG on collapsing regions over at least 50 variants as compared to non-collapsing regions and the average throughout the genome. Results (switch error rates in %) are presented for Chromosome 1 of the real and simulated tetraploid dataset on both 40 × and 80 × coverage. The third row marks the quotient between the switch error rate of H-POPG and that of WHATSHAP POLYPHASE to highlight by which magnitude the results differ

From: Haplotype threading: accurate polyploid phasing from long reads

Coverage

Method

Collapsing regions

Non-collapsing regions

Total

(a) Real read data (tetraploid)

40 ×

WH-PP

0.29

0.69

0.60

 

H-PoPG

2.02

2.16

2.02

 

\(\text {SER}(\frac {\textsc {H-PoPG}}{\textsc {WH-PP}})\)

6.97

3.13

3.37

80 ×

WH-PP

0.14

0.46

0.35

 

H-PoPG

1.05

1.30

1.24

 

\(\text {SER}(\frac {\textsc {H-PoPG}}{\textsc {WH-PP}})\)

7.50

2.83

3.54

(b) Simulated read data (tetraploid)

40 ×

WH-PP

0.18

0.45

0.43

 

H-PoPG

2.01

1.63

1.68

 

\(\text {SER}(\frac {\textsc {H-PoPG}}{\textsc {WH-PP}})\)

11.17

3.62

3.91

80 ×

WH-PP

0.08

0.37

0.32

 

H-PoPG

0.94

0.98

0.99

 

\(\text {SER}(\frac {\textsc {H-PoPG}}{\textsc {WH-PP}})\)

11.75

2.65

3.09