Performance comparison of second- and third-generation sequencers using a bacterial genome with two chromosomes

BMC Genomics

Table 2 Accuracy of assembled contigs with respect to the reference genome

Mismatches	GS Jr	Ion PGM	MiSeq	PacBio	PacBio (>1 M bp)
Number of contigs	309	61	34	31	2
Number of mismatches	133	108	230	389	157
Number of indels	824	2853	184	715	698
Indels length	977	3018	241	818	794
Number of mismatches per 100 kbp	2.6	2.1	4.5	7.5	3.0
Number of indels per 100 kbp	16.3	56.2	3.6	13.8	13.5
Number of misassemblies	0	0	1	13	10
Number of relocations	0	0	1	11	10
Number of translocations	0	0	0	1	0
Number of inversions	0	0	0	1	0
Number of misassembled contigs	0	0	1	5	2
Genome coverage (%)	97.844	98.290	98.499	99.999	99.848
Duplication ratio	1.004	1.000	1.003	1.032	1.007

Generated contigs were compared with the reference genome using QUAST v2.3 [23]. The number of indels is the total number of insertions and deletions in the aligned bases. The number of relocations, inversions, and translocations are classified as misassemblies. A relocation is defined as a misassembly in which the left and right flanking sequences both align to the same chromosome on the reference but are either >1 kb apart or overlap by >1 kb. An inversion is a misassembly in which the left and right flanking sequences both align to the same chromosome but on opposite strands. A translocation is a misassembly in which the flanking sequences align on different chromosomes. Genome coverage is the percentage of bases aligned to the reference genome.

ISSN: 1471-2164