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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