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 Mapped17520198.412%
Wrongly Mapped28271.588%
Not Mapped00.0%
Total178028100.0%
Read Failure Statistics
Not mapped00.0%
Missing in mapper output00.0%
Mapped to wrong chromosome20951.177%
Mapped to wrong position7320.411%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment8
Secondary Alignments0
F-Measure0.992000
Precision0.984100
Recall1.000000
Timing
Raw Mapping Time385.172s
Effective Mapping Time380.956s
Effective Init Time4.216s
Effective Time MeasureCPU
Mapping Time (Wall)108.036s
Mapping Time (CPU)385.172s
Mapping Time (CPU User)376.304s
Mapping Time (CPU System)8.868s
Init Time (Wall)11.828s
Init Time (CPU)4.216s
Init Time (CPU User)0.152s
Init Time (CPU System)4.064s
Additional Information
Mapper Memory Usage4783 MB
Total Test Runtime (Wall)148.213s
Mapper Command Line: 
/project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/Bos_taurus.fa 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/Bos_taurus.fa reads_base.fastq -t 4 > out_bwasw.sam

command/project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/Bos_taurus.fa reads_base.fastq -t 4 > out_bwasw.sam
memory4568628000
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/Bos_taurus.fa reads_base.fastq
[main] Real time: 4.090 sec; CPU: 4.020 sec
systime3.916
time4.1240799427
usrtime0.116
working_directory/project/teaser/genometeaser/tests_generated/14e5e97d9d3c2238f7310baab576d567

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

command/project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/Bos_taurus.fa reads_base.fastq -t 4 > out_bwasw.sam
memory4568756000
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/Bos_taurus.fa reads_base.fastq
[main] Real time: 11.797 sec; CPU: 4.204 sec
systime4.064
time11.8278479576
usrtime0.152
working_directory/project/teaser/genometeaser/tests_generated/14e5e97d9d3c2238f7310baab576d567

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

command/project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/Bos_taurus.fa reads1.fastq reads2.fastq -t 4 > out_bwasw.sam
memory4783000000
return0
status1
stderr
None
stdout
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[bsw2_aln] read 178028 sequences/pairs (26704200 bp) ...
[bsw2_stat] infer the insert size distribution from 19297 high-quality pairs.
[bsw2_stat] (25, 50, 75) percentile: (177, 199, 221)
[bsw2_stat] low and high boundaries for computing mean and std.dev: (150, 309)
[bsw2_stat] mean and std.dev: (200.63, 29.75)
[bsw2_stat] low and high boundaries for proper pairs: (150, 353)
[bsw2_pair] #fixed=343, #rescued=3, #moved=1
[bsw2_stat] infer the insert size distribution from 19241 high-quality pairs.
[bsw2_stat] (25, 50, 75) percentile: (177, 198, 221)
[bsw2_stat] low and high boundaries for computing mean and std.dev: (150, 309)
[bsw2_stat] mean and std.dev: (200.86, 29.85)
[bsw2_stat] low and high boundaries for proper pairs: (150, 353)
[bsw2_pair] #fixed=401, #rescued=3, #moved=6
[bsw2_stat] infer the insert size distribution from 19161 high-quality pairs.
[bsw2_stat] (25, 50, 75) percentile: (177, 198, 220)
[bsw2_stat] low and high boundaries for computing mean and std.dev: (150, 306)
[bsw2_stat] mean and std.dev: (200.45, 29.67)
[bsw2_stat] low and high boundaries for proper pairs: (150, 349)
[bsw2_pair] #fixed=355, #rescued=3, #moved=1
[bsw2_stat] infer the insert size distribution from 19207 high-quality pairs.
[bsw2_stat] (25, 50, 75) percentile: (177, 199, 221)
[bsw2_stat] low and high boundaries for computing mean and std.dev: (150, 309)
[bsw2_stat] mean and std.dev: (200.57, 29.54)
[bsw2_stat] low and high boundaries for proper pairs: (150, 353)
[bsw2_pair] #fixed=401, #rescued=5, #moved=2
[main] Version: 0.7.16a-r1181
[main] CMD: /project/teaser/genometeaser/software/bwa bwasw -t 4 /project/teaser/genometeaser/references/Bos_taurus.fa reads1.fastq reads2.fastq
[main] Real time: 107.991 sec; CPU: 385.160 sec
systime8.868
time108.036365986
usrtime376.304
working_directory/project/teaser/genometeaser/tests_generated/14e5e97d9d3c2238f7310baab576d567