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Table 2 Summary of quality statistics for the R9.4.1 basecalled datasets, in percentages

From: Species-specific basecallers improve actual accuracy of nanopore sequencing in plants

Basecaller model

P. stellatum (R9.4.1)

X. johnsonii

Quality score

Read identity

R2

Quality score

Read identity

R2

Guppy 5 super accurate

86.35%  ± 45.92%

91.96%  ± 3.83%

0.777

90.16%  ± 48.12%

94.15%  ± 3.12%

0.801

Guppy 6 super accurate

86.68%  ± 46.75%

91.96%  ± 3.83%

0.777

90.47%  ± 48.75%

94.15%  ± 3.12%

0.801

Guppy 6 super accurate—plant

84.73%  ± 50.92%

91.47% ± 3.50%

0.850

92.81%  ± 54.60%

96.18% ± 3.50%

0.900

Reciprocal species-specific

93.00%  ± 50.83%

92.98%  ± 3.16%

0.577

95.55%  ± 45.02%

94.43%  ± 2.69%

0.787

Species-specific

94.83%  ± 47.35%

93.24%  ± 3.00%

0.648

95.59%  ± 48.46%

95.16%  ± 2.74%

0.805

  1. Average read quality scores and read identity for all Phebalium stellatum (R9.4.1) and Xanthorrhoea johnsonii basecalled datasets. Average read quality scores were calculated per-read, and the overall average calculated. Read identity is calculated per-read against the HiFi genome and averaged. Averages are shown with standard deviations. For reciprocal species-specific models, P. stellatum reads were basecalled with the X. johnsonii model and X. johnsonii reads were basecalled with the P. stellatum model. R2 values show the correlation between average read quality score and read identity, calculated by linear regression