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 Mapped48606897.484%
Wrongly Mapped125462.516%
Not Mapped00.0%
Total498614100.0%
Read Failure Statistics
Not mapped00.0%
Missing in mapper output00.0%
Mapped to wrong chromosome48860.98%
Mapped to wrong position76601.536%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments0
F-Measure0.987300
Precision0.974800
Recall1.000000
Timing
Raw Mapping Time50.780s
Effective Mapping Time50.584s
Effective Init Time0.196s
Effective Time MeasureCPU
Mapping Time (Wall)23.472s
Mapping Time (CPU)50.780s
Mapping Time (CPU User)49.068s
Mapping Time (CPU System)1.712s
Init Time (Wall)0.268s
Init Time (CPU)0.196s
Init Time (CPU User)0.012s
Init Time (CPU System)0.184s
Additional Information
Mapper Memory Usage524 MB
Total Test Runtime (Wall)83.344s
Mapper Command Line: 
/project/teaser/genometeaser/software/bwa mem /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas reads1.fastq reads2.fastq -t 4 > out_bwamem.sam
Errors and Warnings
No problems were encountered.
Subprocess Log

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

command/project/teaser/genometeaser/software/bwa mem /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas reads_base.fastq -t 4 > out_bwamem.sam
memory209224000
return0
status1
stderr
None
stdout
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 1 sequences (60 bp)...
[M::mem_process_seqs] Processed 1 reads in 0.004 CPU sec, 0.002 real sec
[main] Version: 0.7.16a-r1181
[main] CMD: /project/teaser/genometeaser/software/bwa mem -t 4 /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas reads_base.fastq
[main] Real time: 0.259 sec; CPU: 0.184 sec
systime0.188
time0.285639047623
usrtime0.012
working_directory/project/teaser/genometeaser/tests_generated/340a758089e3620a129e06c436f2f4af

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

command/project/teaser/genometeaser/software/bwa mem /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas reads_base.fastq -t 4 > out_bwamem.sam
memory209216000
return0
status1
stderr
None
stdout
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 1 sequences (60 bp)...
[M::mem_process_seqs] Processed 1 reads in 0.000 CPU sec, 0.002 real sec
[main] Version: 0.7.16a-r1181
[main] CMD: /project/teaser/genometeaser/software/bwa mem -t 4 /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas reads_base.fastq
[main] Real time: 0.235 sec; CPU: 0.184 sec
systime0.184
time0.267585039139
usrtime0.012
working_directory/project/teaser/genometeaser/tests_generated/340a758089e3620a129e06c436f2f4af

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

command/project/teaser/genometeaser/software/bwa mem /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas reads1.fastq reads2.fastq -t 4 > out_bwamem.sam
memory524048000
return0
status1
stderr
None
stdout
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 498614 sequences (29916840 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 214832, 272, 0)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (76, 98, 120)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 208)
[M::mem_pestat] mean and std.dev: (98.27, 32.55)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 252)
[M::mem_pestat] analyzing insert size distribution for orientation RF...
[M::mem_pestat] (25, 50, 75) percentile: (1, 1, 1)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 1)
[M::mem_pestat] mean and std.dev: (1.00, 0.00)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1)
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_pestat] skip orientation RF
[M::mem_process_seqs] Processed 498614 reads in 49.264 CPU sec, 12.557 real sec
[main] Version: 0.7.16a-r1181
[main] CMD: /project/teaser/genometeaser/software/bwa mem -t 4 /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas reads1.fastq reads2.fastq
[main] Real time: 23.418 sec; CPU: 50.768 sec
systime1.712
time23.4720659256
usrtime49.068
working_directory/project/teaser/genometeaser/tests_generated/340a758089e3620a129e06c436f2f4af