Table 3. Effects of error correction on the improved TPA SS14-RS genome with respect to other TPA strains.

	The original SS14 genome (CP000805.1)			SS14-RS genome (CP004011.1)
	Sub	In	Del	Sub	In	Del
Chicago genome (CP001752.1)	346	91	32	332 (96.0%)	17 (18.7%)	15 (46.9%)
DAl-1 genome (CP003115.1)	373	89	95	365 (97.9%)	18 (20.2%)	20 (21.1%)
Mexico A genome (CP003064.1)	175	85	28	91 (52.0%)	16 (18.8%)	11 (39.3%)
The original Nichols genome (AE000520.1)	327	14	18	–	–	–
Nichols-RS genome (CP004010.2)	–	–	–	350 (107.0%)	16 (114.3%)	17 (94.4%)

The left part of the table shows former number of differences between the original TPA SS14 genome (CP000805.1) and other TPA genomes, the right part of the table shows verified number of differences between the improved TPA SS14 genome (CP004011.1) and other TPA genomes. Numbers in brackets show the percentage of verified differences between the improved TPA SS14 genome and other genomes compared to numbers observed during the comparison of the original SS14 genome and other TPA genomes. Because of high sequence diversities, tprD and tprK were excluded from the analyses. Please note that the number of sequence differences between TPA SS14 and Nichols genomes increased after error correction.

sub, substitution; in, insertion; del, deletion.