Table 4.

Comparison of genes with CDS features mapped from T2T-CHM13 to Han1.

Mapped genes with CDS features
Conserved genes (82%)		Altered genes (18%)
Identical	Synonymous	Nonsynonymous	Start lost	Stop gained	Truncated	Frameshift	In-frame insertion	In-frame deletion
14,130	2,442	3,200	21	31	$1+39$ ($5^{\prime }+3^{\prime }$)	143	110	92

For this gene-level analysis, the transcript-to-transcript mapping selected the alignment that produced the highest amino acid identity score for the coding sequence (CDS). Truncated genes are those where the mapped copy is missing either the $5^{\prime }$ end or the $3^{\prime }$ end of the transcript, including the start/stop codon.