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Table 1 Distribution of ASDPs

From: Alternate-locus aware variant calling in whole genome sequencing

ASDP category

Count

Percentage

SNV

187,080

80.5%

Deletion

15,955

6.9%

Deletion (1 nt)

6,368

2.7%

Deletion (2 nt)

2,413

1.0%

Deletion (3–50 nt)

7,174

3.1%

Insertion

15,286

6.6%

Insertion (1 nt)

6,423

2.8%

Insertion (2 nt)

2,224

1.0%

Insertion (3–50 nt)

6,639

2.9%

Block substitution

14,012

6.0%

Block substitution (2 nt)

11,659

5.0%

Block substitution (3 nt)

1,653

0.7%

Block substitution (4–50 nt)

700

0.3%

  1. A total of 232,333 high-quality ASDPs were characterized by our algorithm of which 80.5% corresponded to SNVs when comparing the alternate locus with the corresponding primary assembly. About 7% each were deletions and insertions and 6% were block substitutions with equal numbers of nucleotides.
  2. ASDP alignable scaffold-discrepant position, SNV single nucleotide variant
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Genome Medicine

ISSN: 1756-994X

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