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 Mapped19608498.314%
Wrongly Mapped33611.685%
Not Mapped10.001%
Total199446100.0%
Read Failure Statistics
Not mapped10.001%
Missing in mapper output00.0%
Mapped to wrong chromosome9970.5%
Mapped to wrong position23641.185%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment3
Secondary Alignments0
F-Measure0.991500
Precision0.983100
Recall1.000000
Timing
Raw Mapping Time219.932s
Effective Mapping Time219.752s
Effective Init Time0.180s
Effective Time MeasureCPU
Mapping Time (Wall)80.794s
Mapping Time (CPU)219.932s
Mapping Time (CPU User)216.384s
Mapping Time (CPU System)3.548s
Init Time (Wall)0.339s
Init Time (CPU)0.180s
Init Time (CPU User)0.012s
Init Time (CPU System)0.168s
Additional Information
Mapper Memory Usage447 MB
Total Test Runtime (Wall)131.921s
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
memory207732000
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: 0.650 sec; CPU: 0.272 sec
systime0.272
time0.67391705513
usrtime0.008
working_directory/project/teaser/genometeaser/tests_generated/e1c9b59d61d1a772598b0749ea6b7508

/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
memory207732000
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: 0.314 sec; CPU: 0.172 sec
systime0.168
time0.33908200264
usrtime0.012
working_directory/project/teaser/genometeaser/tests_generated/e1c9b59d61d1a772598b0749ea6b7508

/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
memory447256000
return0
status1
stderr
None
stdout
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[bsw2_aln] read 199446 sequences/pairs (29916900 bp) ...
[bsw2_stat] infer the insert size distribution from 22138 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: (200.53, 29.84)
[bsw2_stat] low and high boundaries for proper pairs: (150, 353)
[bsw2_pair] #fixed=419, #rescued=2, #moved=0
[bsw2_stat] infer the insert size distribution from 22225 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: (200.57, 29.63)
[bsw2_stat] low and high boundaries for proper pairs: (150, 353)
[bsw2_pair] #fixed=370, #rescued=1, #moved=2
[bsw2_stat] infer the insert size distribution from 22188 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: (200.39, 29.71)
[bsw2_stat] low and high boundaries for proper pairs: (150, 353)
[bsw2_pair] #fixed=412, #rescued=0, #moved=1
[bsw2_stat] infer the insert size distribution from 22140 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: (200.38, 29.63)
[bsw2_stat] low and high boundaries for proper pairs: (150, 353)
[bsw2_pair] #fixed=373, #rescued=1, #moved=1
[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: 80.725 sec; CPU: 219.920 sec
systime3.548
time80.7941989899
usrtime216.384
working_directory/project/teaser/genometeaser/tests_generated/e1c9b59d61d1a772598b0749ea6b7508