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 Mapped30114793.361%
Wrongly Mapped213926.632%
Not Mapped220.007%
Total322561100.0%
Read Failure Statistics
Not mapped220.007%
Missing in mapper output00.0%
Mapped to wrong chromosome99213.076%
Mapped to wrong position114713.556%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment17
Secondary Alignments0
F-Measure0.965700
Precision0.933700
Recall0.999900
Timing
Raw Mapping Time201.144s
Effective Mapping Time114.767s
Effective Init Time86.376s
Effective Time MeasureWall clock
Mapping Time (Wall)201.144s
Mapping Time (CPU)490.510s
Mapping Time (CPU User)476.940s
Mapping Time (CPU System)13.570s
Init Time (Wall)86.376s
Init Time (CPU)14.944s
Init Time (CPU User)0.059s
Init Time (CPU System)14.885s
Additional Information
Mapper Memory Usage8592 MB
Total Test Runtime (Wall)387.047s
Mapper Command Line: 
/project2/NextGenMapTest/Teaser/software/bwa bwasw /project2/NextGenMapTest/Teaser/references/m_musculus.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/m_musculus.fasta reads_base.fastq -t 4 > out_bwasw.sam

command/project2/NextGenMapTest/Teaser/software/bwa bwasw /project2/NextGenMapTest/Teaser/references/m_musculus.fasta reads_base.fastq -t 4 > out_bwasw.sam
memory8270632000
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/m_musculus.fasta reads_base.fastq

[main] Real time: 85.437 sec; CPU: 18.913 sec
systime18.866131
time85.4443428516
usrtime0.050992
working_directory/project2/NextGenMapTest/Teaser/tests_generated/M1_n

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

command/project2/NextGenMapTest/Teaser/software/bwa bwasw /project2/NextGenMapTest/Teaser/references/m_musculus.fasta reads_base.fastq -t 4 > out_bwasw.sam
memory8270604000
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/m_musculus.fasta reads_base.fastq

[main] Real time: 86.358 sec; CPU: 14.940 sec
systime14.884737
time86.3761479855
usrtime0.058991
working_directory/project2/NextGenMapTest/Teaser/tests_generated/M1_n

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

command/project2/NextGenMapTest/Teaser/software/bwa bwasw /project2/NextGenMapTest/Teaser/references/m_musculus.fasta reads.fastq -t 4 > out_bwasw.sam
memory8592904000
return0
status1
stderr

None
stdout

[M::bwa_idx_load_from_disk] read 0 ALT contigs

[bsw2_aln] read 266668 sequences/pairs (40000200 bp) ...

[bsw2_aln] read 55893 sequences/pairs (8383950 bp) ...

[main] Version: 0.7.12-r1039

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

[main] Real time: 201.103 sec; CPU: 490.502 sec
systime13.569937
time201.143608093
usrtime476.940494
working_directory/project2/NextGenMapTest/Teaser/tests_generated/M1_n