Mapping Quality Thresholds

The plot below shows the percentages of correctly and wrongly mapped reads for all mapping quality thresholds for this mapper. The values at threshold 0 therefore correspond to the unfiltered results.

Basic Statistics
Correctly Mapped21931091.553%
Wrongly Mapped202318.446%
Not Mapped20.001%
Total239543100.0%
Read Failure Statistics
Not mapped20.001%
Missing in mapper output00.0%
Mapped to wrong chromosome109854.586%
Mapped to wrong position92463.86%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment13
Secondary Alignments0
F-Measure0.955900
Precision0.915500
Recall1.000000
Timing
Raw Mapping Time43.301s
Effective Mapping Time43.179s
Effective Init Time0.122s
Effective Time MeasureWall clock
Mapping Time (Wall)43.301s
Mapping Time (CPU)162.366s
Mapping Time (CPU User)161.307s
Mapping Time (CPU System)1.059s
Init Time (Wall)0.122s
Init Time (CPU)0.071s
Init Time (CPU User)0.008s
Init Time (CPU System)0.063s
Additional Information
Mapper Memory Usage531 MB
Total Test Runtime (Wall)57.856s
Mapper Command Line: 
/project2/NextGenMapTest/Teaser/software/bwa bwasw /project2/NextGenMapTest/Teaser/references/d_melanogaster.fasta reads.fastq -t 4 > out_bwasw.sam
Errors and Warnings
No problems were encountered.
Subprocess Log

/project2/NextGenMapTest/Teaser/software/bwa bwasw /project2/NextGenMapTest/Teaser/references/d_melanogaster.fasta reads_base.fastq -t 4 > out_bwasw.sam

command/project2/NextGenMapTest/Teaser/software/bwa bwasw /project2/NextGenMapTest/Teaser/references/d_melanogaster.fasta reads_base.fastq -t 4 > out_bwasw.sam
memory247432000
return0
status1
stderr

None
stdout

[M::bwa_idx_load_from_disk] read 0 ALT contigs

[bsw2_aln] read 1 sequences/pairs (60 bp) ...

[main] Version: 0.7.12-r1039

[main] CMD: /project2/NextGenMapTest/Teaser/software/bwa bwasw -t 4 /project2/NextGenMapTest/Teaser/references/d_melanogaster.fasta reads_base.fastq

[main] Real time: 2.754 sec; CPU: 0.102 sec
systime0.100984
time2.78899312019
usrtime0.003999
working_directory/project2/NextGenMapTest/Teaser/tests_generated/D1_n

/project2/NextGenMapTest/Teaser/software/bwa bwasw /project2/NextGenMapTest/Teaser/references/d_melanogaster.fasta reads_base.fastq -t 4 > out_bwasw.sam

command/project2/NextGenMapTest/Teaser/software/bwa bwasw /project2/NextGenMapTest/Teaser/references/d_melanogaster.fasta reads_base.fastq -t 4 > out_bwasw.sam
memory247432000
return0
status1
stderr

None
stdout

[M::bwa_idx_load_from_disk] read 0 ALT contigs

[bsw2_aln] read 1 sequences/pairs (60 bp) ...

[main] Version: 0.7.12-r1039

[main] CMD: /project2/NextGenMapTest/Teaser/software/bwa bwasw -t 4 /project2/NextGenMapTest/Teaser/references/d_melanogaster.fasta reads_base.fastq

[main] Real time: 0.116 sec; CPU: 0.067 sec
systime0.06299
time0.121994972229
usrtime0.007998
working_directory/project2/NextGenMapTest/Teaser/tests_generated/D1_n

/project2/NextGenMapTest/Teaser/software/bwa bwasw /project2/NextGenMapTest/Teaser/references/d_melanogaster.fasta reads.fastq -t 4 > out_bwasw.sam

command/project2/NextGenMapTest/Teaser/software/bwa bwasw /project2/NextGenMapTest/Teaser/references/d_melanogaster.fasta reads.fastq -t 4 > out_bwasw.sam
memory531352000
return0
status1
stderr

None
stdout

[M::bwa_idx_load_from_disk] read 0 ALT contigs

[bsw2_aln] read 239543 sequences/pairs (35931450 bp) ...

[main] Version: 0.7.12-r1039

[main] CMD: /project2/NextGenMapTest/Teaser/software/bwa bwasw -t 4 /project2/NextGenMapTest/Teaser/references/d_melanogaster.fasta reads.fastq

[main] Real time: 43.292 sec; CPU: 162.361 sec
systime1.058839
time43.3005189896
usrtime161.307477
working_directory/project2/NextGenMapTest/Teaser/tests_generated/D1_n