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 (1120bp)
Best alignment score: 1120.0 (LEN: 1120, IDY: 100.00), Total number of alignments: 1
		One align captures most of this contig: 1 1120 | 1 1120 | 1120 1120 | 100.0 | gi_49175990_ref_NC_000913.2_ contig1

CONTIG: contig2 (1610bp)
Best alignment score: 1610.0 (LEN: 1610, IDY: 100.00), Total number of alignments: 1
		One align captures most of this contig: 1681 3290 | 1 1610 | 1610 1610 | 100.0 | gi_49175990_ref_NC_000913.2_ contig2

CONTIG: contig3 (3980bp)
Best alignment score: 2030.0 (LEN: 2030, IDY: 100.00), Total number of alignments: 2
			Looking for the best set of alignments (out of 2 total alignments)
			The best set is below. Score: 3779.9, number of alignments: 2, unaligned bases: 0
		This contig is misassembled.
			Excluding internal overlap of size 2 between Alignment 1 and 2: 8049 10000 | 2029 3980 | 1952 1952 --> 8051 10000 | 2031 3980 | 1950 1950
			Real Alignment 1: 4621 6650 | 1 2030 | 2030 2030 | 100.0 | gi_49175990_ref_NC_000913.2_ contig3
			  Extensive misassembly (relocation, inconsistency = 1400) between these two alignments
			Real Alignment 2: 8051 10000 | 2031 3980 | 1950 1950 | 100.0 | gi_49175990_ref_NC_000913.2_ contig3

Analyzing coverage...
Writing SNPs into /home/psgendb/BIRCHDEV/install/quast-5.2.0/quast_test_output/contigs_reports/minimap_output/contigs_1.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_1.used_snps

Results:
	Local Misassemblies: 0
	Misassemblies: 1
		Relocations: 1
		Translocations: 0
		Inversions: 0
	Scaffold gap extensive misassemblies: 0
	Scaffold gap local misassemblies: 0
	Misassembled Contigs: 1
	Misassembled Contig Bases: 3980
	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: 6710
	Raw Aligned Bases in Assembly: 6710
	Total Aligned Bases in Assembly (with "Extras"): 6710

	SNPs: 0
	Insertions: 0
	Deletions: 0