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 Mapped54121190.374%
Wrongly Mapped572439.559%
Not Mapped4040.067%
Total598858100.0%
Read Failure Statistics
Not mapped4040.067%
Missing in mapper output00.0%
Mapped to wrong chromosome314015.243%
Mapped to wrong position258424.315%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments0
F-Measure0.949400
Precision0.904300
Recall0.999300
Timing
Raw Mapping Time312.296s
Effective Mapping Time310.572s
Effective Init Time1.724s
Effective Time MeasureCPU
Mapping Time (Wall)82.366s
Mapping Time (CPU)312.296s
Mapping Time (CPU User)306.772s
Mapping Time (CPU System)5.524s
Init Time (Wall)1.723s
Init Time (CPU)1.724s
Init Time (CPU User)0.176s
Init Time (CPU System)1.548s
Additional Information
Mapper Memory Usage250 MB
Total Test Runtime (Wall)211.750s
Mapper Command Line: 
/project/teaser/genometeaser/software/bowtie2/bowtie2 -p 4 -x /project/teaser/genometeaser/references/D_melanogaster.fasta_bt -1 reads1.fastq -2 reads2.fastq -S out_bowtie2.sam
Errors and Warnings
No problems were encountered.
Subprocess Log

/project/teaser/genometeaser/software/bowtie2/bowtie2 -p 4 -x /project/teaser/genometeaser/references/D_melanogaster.fasta_bt -U reads_base.fastq -S out_bowtie2.sam

command/project/teaser/genometeaser/software/bowtie2/bowtie2 -p 4 -x /project/teaser/genometeaser/references/D_melanogaster.fasta_bt -U reads_base.fastq -S out_bowtie2.sam
memory220900000
return0
status1
stderr
None
stdout
1 reads; of these:
1 (100.00%) were unpaired; of these:
1 (100.00%) aligned 0 times
0 (0.00%) aligned exactly 1 time
0 (0.00%) aligned >1 times
0.00% overall alignment rate
systime1.38
time16.0028021336
usrtime0.152
working_directory/project/teaser/genometeaser/tests_generated/dc51ba987f7f2a219710af74d49a4380

/project/teaser/genometeaser/software/bowtie2/bowtie2 -p 4 -x /project/teaser/genometeaser/references/D_melanogaster.fasta_bt -U reads_base.fastq -S out_bowtie2.sam

command/project/teaser/genometeaser/software/bowtie2/bowtie2 -p 4 -x /project/teaser/genometeaser/references/D_melanogaster.fasta_bt -U reads_base.fastq -S out_bowtie2.sam
memory221992000
return0
status1
stderr
None
stdout
1 reads; of these:
1 (100.00%) were unpaired; of these:
1 (100.00%) aligned 0 times
0 (0.00%) aligned exactly 1 time
0 (0.00%) aligned >1 times
0.00% overall alignment rate
systime1.548
time1.7226369381
usrtime0.176
working_directory/project/teaser/genometeaser/tests_generated/dc51ba987f7f2a219710af74d49a4380

/project/teaser/genometeaser/software/bowtie2/bowtie2 -p 4 -x /project/teaser/genometeaser/references/D_melanogaster.fasta_bt -1 reads1.fastq -2 reads2.fastq -S out_bowtie2.sam

command/project/teaser/genometeaser/software/bowtie2/bowtie2 -p 4 -x /project/teaser/genometeaser/references/D_melanogaster.fasta_bt -1 reads1.fastq -2 reads2.fastq -S out_bowtie2.sam
memory250292000
return0
status1
stderr
None
stdout
299429 reads; of these:
299429 (100.00%) were paired; of these:
33521 (11.19%) aligned concordantly 0 times
220306 (73.58%) aligned concordantly exactly 1 time
45602 (15.23%) aligned concordantly >1 times
----
33521 pairs aligned concordantly 0 times; of these:
27567 (82.24%) aligned discordantly 1 time
----
5954 pairs aligned 0 times concordantly or discordantly; of these:
11908 mates make up the pairs; of these:
404 (3.39%) aligned 0 times
234 (1.97%) aligned exactly 1 time
11270 (94.64%) aligned >1 times
99.93% overall alignment rate
systime5.524
time82.36632514
usrtime306.772
working_directory/project/teaser/genometeaser/tests_generated/dc51ba987f7f2a219710af74d49a4380