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 Mapped14433696.224%
Wrongly Mapped56273.751%
Not Mapped370.025%
Total150000100.0%
Read Failure Statistics
Not mapped370.025%
Missing in mapper output00.0%
Mapped to wrong chromosome00.0%
Mapped to wrong position56273.751%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment4
Secondary Alignments0
F-Measure0.980800
Precision0.962500
Recall0.999700
Timing
Raw Mapping Time11.775s
Effective Mapping Time11.580s
Effective Init Time0.195s
Effective Time MeasureWall clock
Mapping Time (Wall)11.775s
Mapping Time (CPU)43.957s
Mapping Time (CPU User)43.400s
Mapping Time (CPU System)0.557s
Init Time (Wall)0.195s
Init Time (CPU)0.014s
Init Time (CPU User)0.002s
Init Time (CPU System)0.012s
Additional Information
Mapper Memory Usage170 MB
Total Test Runtime (Wall)19.389s
Mapper Command Line: 
/project2/NextGenMapTest/Teaser/software/bwa bwasw /project2/NextGenMapTest/Teaser/references/E_coli.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/E_coli.fasta reads_base.fastq -t 4 > out_bwasw.sam

command/project2/NextGenMapTest/Teaser/software/bwa bwasw /project2/NextGenMapTest/Teaser/references/E_coli.fasta reads_base.fastq -t 4 > out_bwasw.sam
memory19296000
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/E_coli.fasta reads_base.fastq

[main] Real time: 0.009 sec; CPU: 0.006 sec
systime0.007998
time0.0141520500183
usrtime0.000999
working_directory/project2/NextGenMapTest/Teaser/tests_generated/ecoli_test

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

command/project2/NextGenMapTest/Teaser/software/bwa bwasw /project2/NextGenMapTest/Teaser/references/E_coli.fasta reads_base.fastq -t 4 > out_bwasw.sam
memory19296000
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/E_coli.fasta reads_base.fastq

[main] Real time: 0.101 sec; CPU: 0.012 sec
systime0.011998
time0.195190906525
usrtime0.001999
working_directory/project2/NextGenMapTest/Teaser/tests_generated/ecoli_test

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

command/project2/NextGenMapTest/Teaser/software/bwa bwasw /project2/NextGenMapTest/Teaser/references/E_coli.fasta reads.fastq -t 4 > out_bwasw.sam
memory170060000
return0
status1
stderr

None
stdout

[M::bwa_idx_load_from_disk] read 0 ALT contigs

[bsw2_aln] read 150000 sequences/pairs (15000000 bp) ...

[main] Version: 0.7.12-r1039

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

[main] Real time: 11.768 sec; CPU: 43.952 sec
systime0.556915
time11.7753069401
usrtime43.400402
working_directory/project2/NextGenMapTest/Teaser/tests_generated/ecoli_test