Table 1. Results for error correction by POLCA and Pilon on an A. thaliana genome (total size 119Mb) with three different numbers of simulated errors.

Error rates ranged from 0.1% to 0.46%. Boldface indicates the better values for each experiment in each row.

	POLCA			Pilon
Experiment (error rate)	Exp 1 (0.1%)	Exp 2 (0.2%)	Exp 3 (0.46%)	Exp 1 (0.1%)	Exp 2 (0.2%)	Exp 3 (0.46%)
Simulated substitution errors	53,726	107,244	267,896	53,726	107,244	267,896
Substitutions fixed (TP)	48,442	97,093	241,883	49,545	98,825	246,405
Substitutions missed (FN)	5,284	10,151	26,013	4,181	8,419	21,491
Substitution errors introduced (FP)	4	27	68	2,019	3,887	9,471
Simulated indel errors	57,758	112,894	281,332	57,758	112,894	281,332
Indels fixed (TP)	54,802	107,588	268,702	55,463	107,576	261,279
Indels missed (FN)	2,956	5,306	12,630	2,295	5,318	20,053
Indel errors introduced (FP)	237	708	1,560	2,796	5,543	19,177
Total errors remaining after polishing	8,481	16,192	40,271	11,291	23,167	70,192