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 Mapped24608698.434%
Wrongly Mapped36451.458%
Not Mapped2690.108%
Total250000100.0%
Read Failure Statistics
Not mapped2690.108%
Missing in mapper output00.0%
Mapped to wrong chromosome28981.159%
Mapped to wrong position7470.299%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment2
Secondary Alignments0
F-Measure0.992100
Precision0.985400
Recall0.998900
Timing
Raw Mapping Time70.319s
Effective Mapping Time70.295s
Effective Init Time0.024s
Effective Time MeasureCPU
Mapping Time (Wall)22.156s
Mapping Time (CPU)70.319s
Mapping Time (CPU User)69.626s
Mapping Time (CPU System)0.693s
Init Time (Wall)0.258s
Init Time (CPU)0.024s
Init Time (CPU User)0.006s
Init Time (CPU System)0.018s
Additional Information
Mapper Memory Usage199 MB
Total Test Runtime (Wall)35.077s
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
memory23788000
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: /project/teaser/genometeaser/software/bwa bwasw -t 4 /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta reads_base.fastq
[main] Real time: 0.054 sec; CPU: 0.019 sec
systime0.018997
time0.0605549812317
usrtime0.004999
working_directory/project/teaser/genometeaser/tests_generated/a1196814bed1e8498427aa17a7703943

/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
memory23788000
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: /project/teaser/genometeaser/software/bwa bwasw -t 4 /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta reads_base.fastq
[main] Real time: 0.179 sec; CPU: 0.020 sec
systime0.017997
time0.257614850998
usrtime0.005999
working_directory/project/teaser/genometeaser/tests_generated/a1196814bed1e8498427aa17a7703943

/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
memory199176000
return0
status1
stderr
None
stdout
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[bsw2_aln] read 250000 sequences/pairs (15000000 bp) ...
[bsw2_stat] infer the insert size distribution from 28917 high-quality pairs.
[bsw2_stat] (25, 50, 75) percentile: (80, 99, 121)
[bsw2_stat] low and high boundaries for computing mean and std.dev: (60, 203)
[bsw2_stat] mean and std.dev: (102.29, 27.65)
[bsw2_stat] low and high boundaries for proper pairs: (60, 244)
[bsw2_pair] #fixed=2290, #rescued=1189, #moved=15
[bsw2_stat] infer the insert size distribution from 28788 high-quality pairs.
[bsw2_stat] (25, 50, 75) percentile: (80, 99, 121)
[bsw2_stat] low and high boundaries for computing mean and std.dev: (60, 203)
[bsw2_stat] mean and std.dev: (102.40, 27.52)
[bsw2_stat] low and high boundaries for proper pairs: (60, 244)
[bsw2_pair] #fixed=2158, #rescued=1286, #moved=19
[bsw2_stat] infer the insert size distribution from 28871 high-quality pairs.
[bsw2_stat] (25, 50, 75) percentile: (80, 99, 121)
[bsw2_stat] low and high boundaries for computing mean and std.dev: (60, 203)
[bsw2_stat] mean and std.dev: (102.48, 27.49)
[bsw2_stat] low and high boundaries for proper pairs: (60, 244)
[bsw2_pair] #fixed=2217, #rescued=1209, #moved=19
[bsw2_stat] infer the insert size distribution from 28798 high-quality pairs.
[bsw2_stat] (25, 50, 75) percentile: (79, 99, 120)
[bsw2_stat] low and high boundaries for computing mean and std.dev: (60, 202)
[bsw2_stat] mean and std.dev: (102.04, 27.54)
[bsw2_stat] low and high boundaries for proper pairs: (60, 243)
[bsw2_pair] #fixed=2233, #rescued=1295, #moved=16
[main] Version: 0.7.12-r1039
[main] CMD: /project/teaser/genometeaser/software/bwa bwasw -t 4 /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta reads1.fastq reads2.fastq
[main] Real time: 22.143 sec; CPU: 70.308 sec
systime0.692894
time22.1562688351
usrtime69.626415
working_directory/project/teaser/genometeaser/tests_generated/a1196814bed1e8498427aa17a7703943