Aligning contigs to reference...
	Aligning contigs to the reference
Filtering alignments...
Parsing coords...
Loading reference...
	Loaded [gi_49175990_ref_NC_000913.2_]
	Total Regions: 1
	Total Region Length: 10000
Analyzing contigs...
CONTIG: contig1 (2100bp)
Best alignment score: 2100.0 (LEN: 2100, IDY: 100.00), Total number of alignments: 1
		One align captures most of this contig: 1121 3220 | 1 2100 | 2100 2100 | 100.0 | gi_49175990_ref_NC_000913.2_ contig1

CONTIG: contig2 (3360bp)
Best alignment score: 1471.0 (LEN: 1471, IDY: 100.00), Total number of alignments: 3
			Looking for the best set of alignments (out of 3 total alignments)
			The best set is below. Score: 3023.2, number of alignments: 3, unaligned bases: 0
		This contig is misassembled.
			Real Alignment 1: 3431 4130 | 1 700 | 700 700 | 100.0 | gi_49175990_ref_NC_000913.2_ contig2
			  Extensive misassembly (relocation, inconsistency = 1750) between these two alignments
			Excluding internal overlap of size 1 between Alignment 2 and 3: 5881 7070 | 701 1890 | 1190 1190 --> 5881 7069 | 701 1889 | 1189 1189
			Real Alignment 2: 5881 7069 | 701 1889 | 1189 1189 | 100.0 | gi_49175990_ref_NC_000913.2_ contig2
			  Extensive misassembly (relocation, inconsistency = 1050) between these two alignments
			Real Alignment 3: 8120 9590 | 1890 3360 | 1471 1471 | 100.0 | gi_49175990_ref_NC_000913.2_ contig2

Analyzing coverage...
Writing SNPs into /home/psgendb/BIRCHDEV/install/quast-5.2.0/quast_test_output/contigs_reports/minimap_output/contigs_2.used_snps

Analysis is finished!
Founded SNPs were written into /home/psgendb/BIRCHDEV/install/quast-5.2.0/quast_test_output/contigs_reports/minimap_output/contigs_2.used_snps

Results:
	Local Misassemblies: 0
	Misassemblies: 2
		Relocations: 2
		Translocations: 0
		Inversions: 0
	Scaffold gap extensive misassemblies: 0
	Scaffold gap local misassemblies: 0
	Misassembled Contigs: 1
	Misassembled Contig Bases: 3360
	Misassemblies Inter-Contig Overlap ("Extra" Aligned Bases): 0
Unaligned Contigs: 0 + 0 part
Half Unaligned Contigs with Misassemblies: 0
Unaligned Bases in Fully and Partially Unaligned Contigs: 0

Ambiguously Mapped Contigs: 0
Total Bases in Ambiguously Mapped Contigs: 0
"Extra" Aligned Bases in Ambiguously Mapped Contigs: 0
Note that --allow-ambiguity option was set to "one" and only first alignment per each of these contigs was used (there is no "extra" aligned bases).

	Covered Bases in Reference: 5460
	Raw Aligned Bases in Assembly: 5459
	Total Aligned Bases in Assembly (with "Extras"): 5459

	SNPs: 0
	Insertions: 0
	Deletions: 0