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 Mapped48078796.425%
Wrongly Mapped170683.423%
Not Mapped7590.152%
Total498614100.0%
Read Failure Statistics
Not mapped7590.152%
Missing in mapper output00.0%
Mapped to wrong chromosome77071.546%
Mapped to wrong position93611.877%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment3
Secondary Alignments0
F-Measure0.981800
Precision0.965700
Recall0.998400
Timing
Raw Mapping Time197.340s
Effective Mapping Time197.144s
Effective Init Time0.196s
Effective Time MeasureCPU
Mapping Time (Wall)87.458s
Mapping Time (CPU)197.340s
Mapping Time (CPU User)188.780s
Mapping Time (CPU System)8.560s
Init Time (Wall)0.282s
Init Time (CPU)0.196s
Init Time (CPU User)0.000s
Init Time (CPU System)0.196s
Additional Information
Mapper Memory Usage578 MB
Total Test Runtime (Wall)147.791s
Mapper Command Line: 
/project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas 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/Arabidopsis_thaliana.fas reads_base.fastq -t 4 > out_bwasw.sam

command/project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas reads_base.fastq -t 4 > out_bwasw.sam
memory209224000
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/Arabidopsis_thaliana.fas reads_base.fastq
[main] Real time: 0.257 sec; CPU: 0.184 sec
systime0.192
time0.288578033447
usrtime0.004
working_directory/project/teaser/genometeaser/tests_generated/340a758089e3620a129e06c436f2f4af

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

command/project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas reads_base.fastq -t 4 > out_bwasw.sam
memory207600000
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/Arabidopsis_thaliana.fas reads_base.fastq
[main] Real time: 0.251 sec; CPU: 0.184 sec
systime0.196
time0.282344102859
usrtime0.0
working_directory/project/teaser/genometeaser/tests_generated/340a758089e3620a129e06c436f2f4af

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

command/project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas reads1.fastq reads2.fastq -t 4 > out_bwasw.sam
memory578048000
return0
status1
stderr
None
stdout
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[bsw2_aln] read 498614 sequences/pairs (29916840 bp) ...
[bsw2_stat] infer the insert size distribution from 51745 high-quality pairs.
[bsw2_stat] (25, 50, 75) percentile: (80, 100, 121)
[bsw2_stat] low and high boundaries for computing mean and std.dev: (60, 203)
[bsw2_stat] mean and std.dev: (102.60, 27.60)
[bsw2_stat] low and high boundaries for proper pairs: (60, 244)
[bsw2_pair] #fixed=4559, #rescued=3007, #moved=136
[bsw2_stat] infer the insert size distribution from 51608 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: (102.74, 27.82)
[bsw2_stat] low and high boundaries for proper pairs: (60, 244)
[bsw2_pair] #fixed=4699, #rescued=3110, #moved=136
[bsw2_stat] infer the insert size distribution from 51591 high-quality pairs.
[bsw2_stat] (25, 50, 75) percentile: (80, 100, 121)
[bsw2_stat] low and high boundaries for computing mean and std.dev: (60, 203)
[bsw2_stat] mean and std.dev: (102.79, 27.73)
[bsw2_stat] low and high boundaries for proper pairs: (60, 244)
[bsw2_pair] #fixed=4538, #rescued=3107, #moved=126
[bsw2_stat] infer the insert size distribution from 51692 high-quality pairs.
[bsw2_stat] (25, 50, 75) percentile: (80, 100, 121)
[bsw2_stat] low and high boundaries for computing mean and std.dev: (60, 203)
[bsw2_stat] mean and std.dev: (102.59, 27.70)
[bsw2_stat] low and high boundaries for proper pairs: (60, 244)
[bsw2_pair] #fixed=4620, #rescued=3010, #moved=130
[main] Version: 0.7.16a-r1181
[main] CMD: /project/teaser/genometeaser/software/bwa bwasw -t 4 /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas reads1.fastq reads2.fastq
[main] Real time: 87.411 sec; CPU: 197.328 sec
systime8.56
time87.4584758282
usrtime188.78
working_directory/project/teaser/genometeaser/tests_generated/340a758089e3620a129e06c436f2f4af