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 Mapped29647391.912%
Wrongly Mapped258598.017%
Not Mapped2290.071%
Total322561100.0%
Read Failure Statistics
Not mapped2290.071%
Missing in mapper output00.0%
Mapped to wrong chromosome136374.228%
Mapped to wrong position122223.789%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments207
F-Measure0.957900
Precision0.919800
Recall0.999200
Timing
Raw Mapping Time172.796s
Effective Mapping Time105.788s
Effective Init Time67.008s
Effective Time MeasureWall clock
Mapping Time (Wall)172.796s
Mapping Time (CPU)441.126s
Mapping Time (CPU User)428.131s
Mapping Time (CPU System)12.995s
Init Time (Wall)67.008s
Init Time (CPU)12.606s
Init Time (CPU User)0.038s
Init Time (CPU System)12.568s
Additional Information
Mapper Memory Usage9215 MB
Total Test Runtime (Wall)336.905s
Mapper Command Line: 
/project2/NextGenMapTest/Teaser/software/bwa mem /project2/NextGenMapTest/Teaser/references/m_musculus.fasta reads.fastq -t 4 > out_bwamem.sam
Errors and Warnings
No problems were encountered.
Subprocess Log

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

command/project2/NextGenMapTest/Teaser/software/bwa mem /project2/NextGenMapTest/Teaser/references/m_musculus.fasta reads_base.fastq -t 4 > out_bwamem.sam
memory8270148000
return0
status1
stderr

None
stdout

[M::bwa_idx_load_from_disk] read 0 ALT contigs

[M::process] read 1 sequences (60 bp)...

[M::mem_process_seqs] Processed 1 reads in 0.002 CPU sec, 0.040 real sec

[main] Version: 0.7.12-r1039

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

[main] Real time: 76.006 sec; CPU: 15.407 sec
systime15.372663
time76.0443799496
usrtime0.036994
working_directory/project2/NextGenMapTest/Teaser/tests_generated/M2_n

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

command/project2/NextGenMapTest/Teaser/software/bwa mem /project2/NextGenMapTest/Teaser/references/m_musculus.fasta reads_base.fastq -t 4 > out_bwamem.sam
memory8268504000
return0
status1
stderr

None
stdout

[M::bwa_idx_load_from_disk] read 0 ALT contigs

[M::process] read 1 sequences (60 bp)...

[M::mem_process_seqs] Processed 1 reads in 0.003 CPU sec, 0.006 real sec

[main] Version: 0.7.12-r1039

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

[main] Real time: 66.936 sec; CPU: 12.603 sec
systime12.568089
time67.0081889629
usrtime0.037994
working_directory/project2/NextGenMapTest/Teaser/tests_generated/M2_n

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

command/project2/NextGenMapTest/Teaser/software/bwa mem /project2/NextGenMapTest/Teaser/references/m_musculus.fasta reads.fastq -t 4 > out_bwamem.sam
memory9215980000
return0
status1
stderr

None
stdout

[M::bwa_idx_load_from_disk] read 0 ALT contigs

[M::process] read 266668 sequences (40000200 bp)...

[M::process] read 55893 sequences (8383950 bp)...

[M::mem_process_seqs] Processed 266668 reads in 353.733 CPU sec, 88.964 real sec

[M::mem_process_seqs] Processed 55893 reads in 74.603 CPU sec, 18.745 real sec

[main] Version: 0.7.12-r1039

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

[main] Real time: 172.755 sec; CPU: 441.108 sec
systime12.995024
time172.796026945
usrtime428.130914
working_directory/project2/NextGenMapTest/Teaser/tests_generated/M2_n