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 Mapped20883887.182%
Wrongly Mapped209628.751%
Not Mapped97434.067%
Total239543100.0%
Read Failure Statistics
Not mapped97434.067%
Missing in mapper output00.0%
Mapped to wrong chromosome120925.048%
Mapped to wrong position88703.703%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment290
Secondary Alignments0
F-Measure0.931500
Precision0.908800
Recall0.955400
Timing
Raw Mapping Time35.738s
Effective Mapping Time35.596s
Effective Init Time0.142s
Effective Time MeasureWall clock
Mapping Time (Wall)35.738s
Mapping Time (CPU)132.656s
Mapping Time (CPU User)131.572s
Mapping Time (CPU System)1.084s
Init Time (Wall)0.142s
Init Time (CPU)0.060s
Init Time (CPU User)0.004s
Init Time (CPU System)0.056s
Additional Information
Mapper Memory Usage534 MB
Total Test Runtime (Wall)52.754s
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
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: 0.063 sec; CPU: 0.058 sec
systime0.055991
time0.0888237953186
usrtime0.004999
working_directory/project2/NextGenMapTest/Teaser/tests_generated/D2_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: 0.062 sec; CPU: 0.057 sec
systime0.055991
time0.142100095749
usrtime0.003999
working_directory/project2/NextGenMapTest/Teaser/tests_generated/D2_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
memory534232000
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: 35.721 sec; CPU: 132.649 sec
systime1.083835
time35.7378649712
usrtime131.571998
working_directory/project2/NextGenMapTest/Teaser/tests_generated/D2_n