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 Mapped9783954.459%
Wrongly Mapped140557.823%
Not Mapped6776337.718%
Total179657100.0%
Read Failure Statistics
Not mapped6675437.156%
Missing in mapper output10090.562%
Mapped to wrong chromosome71413.975%
Mapped to wrong position69143.848%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment1788
Secondary Alignments0
F-Measure0.707700
Precision0.874400
Recall0.594400
Timing
Raw Mapping Time27.900s
Effective Mapping Time27.832s
Effective Init Time0.068s
Effective Time MeasureWall clock
Mapping Time (Wall)27.900s
Mapping Time (CPU)102.197s
Mapping Time (CPU User)101.425s
Mapping Time (CPU System)0.773s
Init Time (Wall)0.068s
Init Time (CPU)0.060s
Init Time (CPU User)0.006s
Init Time (CPU System)0.054s
Additional Information
Mapper Memory Usage572 MB
Total Test Runtime (Wall)36.423s
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: 0.065 sec; CPU: 0.060 sec
systime0.05999
time0.0709359645844
usrtime0.003999
working_directory/project2/NextGenMapTest/Teaser/tests_generated/D3_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
memory247436000
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: 0.062 sec; CPU: 0.057 sec
systime0.053991
time0.0680348873138
usrtime0.005999
working_directory/project2/NextGenMapTest/Teaser/tests_generated/D3_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
memory572484000
return0
status1
stderr

None
stdout

[M::bwa_idx_load_from_disk] read 0 ALT contigs

[bsw2_aln] read 179657 sequences/pairs (38492672 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: 27.891 sec; CPU: 102.190 sec
systime0.772882
time27.9004371166
usrtime101.424581
working_directory/project2/NextGenMapTest/Teaser/tests_generated/D3_n