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 Mapped9909099.09%
Wrongly Mapped9100.91%
Not Mapped00.0%
Total100000100.0%
Read Failure Statistics
Not mapped00.0%
Missing in mapper output00.0%
Mapped to wrong chromosome6500.65%
Mapped to wrong position2600.26%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments0
F-Measure0.995400
Precision0.990900
Recall1.000000
Timing
Raw Mapping Time116.016s
Effective Mapping Time115.968s
Effective Init Time0.048s
Effective Time MeasureCPU
Mapping Time (Wall)44.655s
Mapping Time (CPU)116.016s
Mapping Time (CPU User)113.936s
Mapping Time (CPU System)2.080s
Init Time (Wall)0.114s
Init Time (CPU)0.048s
Init Time (CPU User)0.012s
Init Time (CPU System)0.036s
Additional Information
Mapper Memory Usage142 MB
Total Test Runtime (Wall)62.410s
Mapper Command Line: 
/project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta reads1.fastq reads2.fastq -t 4 > out_bwasw.sam
Errors and Warnings
No problems were encountered.
Subprocess Log

/project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta reads_base.fastq -t 4 > out_bwasw.sam

command/project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta reads_base.fastq -t 4 > out_bwasw.sam
memory24532000
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: 0.7.16a-r1181
[main] CMD: /project/teaser/genometeaser/software/bwa bwasw -t 4 /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta reads_base.fastq
[main] Real time: 0.064 sec; CPU: 0.040 sec
systime0.032
time0.230095148087
usrtime0.016
working_directory/project/teaser/genometeaser/tests_generated/fea6b65881b1ab0892566fb478a26e05

/project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta reads_base.fastq -t 4 > out_bwasw.sam

command/project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta reads_base.fastq -t 4 > out_bwasw.sam
memory24616000
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: 0.7.16a-r1181
[main] CMD: /project/teaser/genometeaser/software/bwa bwasw -t 4 /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta reads_base.fastq
[main] Real time: 0.073 sec; CPU: 0.040 sec
systime0.036
time0.11443901062
usrtime0.012
working_directory/project/teaser/genometeaser/tests_generated/fea6b65881b1ab0892566fb478a26e05

/project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta reads1.fastq reads2.fastq -t 4 > out_bwasw.sam

command/project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta reads1.fastq reads2.fastq -t 4 > out_bwasw.sam
memory142908000
return0
status1
stderr
None
stdout
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[bsw2_aln] read 100000 sequences/pairs (15000000 bp) ...
[bsw2_stat] infer the insert size distribution from 12036 high-quality pairs.
[bsw2_stat] (25, 50, 75) percentile: (427, 450, 471)
[bsw2_stat] low and high boundaries for computing mean and std.dev: (339, 559)
[bsw2_stat] mean and std.dev: (449.46, 33.00)
[bsw2_stat] low and high boundaries for proper pairs: (295, 603)
[bsw2_pair] #fixed=2567, #rescued=0, #moved=16
[bsw2_stat] infer the insert size distribution from 12014 high-quality pairs.
[bsw2_stat] (25, 50, 75) percentile: (426, 449, 471)
[bsw2_stat] low and high boundaries for computing mean and std.dev: (336, 561)
[bsw2_stat] mean and std.dev: (448.66, 33.00)
[bsw2_stat] low and high boundaries for proper pairs: (291, 606)
[bsw2_pair] #fixed=2707, #rescued=0, #moved=13
[bsw2_stat] infer the insert size distribution from 12059 high-quality pairs.
[bsw2_stat] (25, 50, 75) percentile: (427, 450, 471)
[bsw2_stat] low and high boundaries for computing mean and std.dev: (339, 559)
[bsw2_stat] mean and std.dev: (449.75, 32.74)
[bsw2_stat] low and high boundaries for proper pairs: (295, 603)
[bsw2_pair] #fixed=2685, #rescued=0, #moved=8
[bsw2_stat] infer the insert size distribution from 12101 high-quality pairs.
[bsw2_stat] (25, 50, 75) percentile: (427, 450, 473)
[bsw2_stat] low and high boundaries for computing mean and std.dev: (335, 565)
[bsw2_stat] mean and std.dev: (449.65, 33.01)
[bsw2_stat] low and high boundaries for proper pairs: (289, 611)
[bsw2_pair] #fixed=2643, #rescued=0, #moved=15
[main] Version: 0.7.16a-r1181
[main] CMD: /project/teaser/genometeaser/software/bwa bwasw -t 4 /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta reads1.fastq reads2.fastq
[main] Real time: 44.536 sec; CPU: 115.996 sec
systime2.08
time44.6550869942
usrtime113.936
working_directory/project/teaser/genometeaser/tests_generated/fea6b65881b1ab0892566fb478a26e05