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Table 3 The estimation of the normal/abnormal repeat status of CAG repeats in ATXN3 according to RepeatHMM-DB compared with the determination by prior literature knowledge of normal repeat range

From: Genome-wide detection of short tandem repeat expansions by long-read sequencing

Subject True counts Prior knowledge RepeatHMM-DB
Allele Subject Score Allele Subject
SRR5363334 14, 77 N, P P  − 2.2, 8.4 N, P P
SRR5363452 30, 66 N, P P 0.5, 6.6 N, P P
SRR5363453 14, 69 N, P P  − 2.2, 7.1 N, P P
SRR5363454 14, 71 N, P P  − 2.2, 7.4 N, P P
SRR5363455 21, 72 N, P P  − 1.0, 7.6 N, P P
SRR5363456 14, 77 N, P P  − 2.2, 8.4 N, P P
SRR5363457 26, 71 N, P P  − 0.2, 7.4 N, P P
SRR5363458 14, 63 N, P P  − 2.2, 6.1 N, P P
SRR5363459 29, 70 N, P P 0.3, 7.2 N, P P
SRR5363460 27, 71 N, P P 0.0, 7.4 N, P P
SRR5363461 34, 75 N, P P 1.2, 8.1 N, P P
SRR5363462 28, 89 N, P P 0.2, 10.4 N, P P
SRR5363463 61, 61 P, P P 5.7, 5.7 P, P P
SRR5363464 26, 65 N, P P  − 0.2, 6.4 N, P P
SRR5363465 14, 89 N, P P  − 2.2, 10.4 N, P P
SRR5363466 40, 67 P, P P 2.2, 6.7 P, P P
SRR5363467 37, 68 N, P P 1.7, 6.9 N, P P
SRR5363468 28, 40 N, P P 0.2, 2.2 N, P P
SRR5363469 14, 82 N, P P  − 2.2, 9.2 N, P P
SRR5363470 14, 68 N, P P  − 2.2, 6.9 N, P P
SRR5363471 14, 14 N, N N  − 2.2, − 2.2 N, N N
SRR5363472 27, 35 N, N N 0.0, 1.3 N, N N
SRR5363473 28, 28 N, N N 0.2, 0.2 N, N N
SRR5363480 14, 14 N, N N  − 2.2, − 2.2 N, N N
SRR5363632 14, 19 N, N N  − 2.2, − 1.3 N, N N
  1. The true repeat counts for 20 patients with SCA3 and 5 control subjects were determined by capillary electrophoresis or Sanger sequencing. The estimated normal repeat range of CAG repeat is 11–28. The ‘Allele’ column shows the pathogenic inference for each allele, while the ‘Subject” column shows the disease status prediction for each subject. ‘N’: normal, ‘P’: pathogenic/patient