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 Mapped16396092.176%
Wrongly Mapped139137.822%
Not Mapped50.003%
Total177878100.0%
Read Failure Statistics
Not mapped50.003%
Missing in mapper output00.0%
Mapped to wrong chromosome70163.944%
Mapped to wrong position68973.877%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments0
F-Measure0.959300
Precision0.921800
Recall1.000000
Timing
Raw Mapping Time224.776s
Effective Mapping Time221.448s
Effective Init Time3.328s
Effective Time MeasureCPU
Mapping Time (Wall)63.455s
Mapping Time (CPU)224.776s
Mapping Time (CPU User)216.208s
Mapping Time (CPU System)8.568s
Init Time (Wall)3.428s
Init Time (CPU)3.328s
Init Time (CPU User)0.100s
Init Time (CPU System)3.228s
Additional Information
Mapper Memory Usage283 MB
Total Test Runtime (Wall)132.040s
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
memory221936000
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
systime6.924
time16.3389108181
usrtime0.156
working_directory/project/teaser/genometeaser/tests_generated/e06f9a576d69697f7ad166f2c53eac4f

/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
memory220060000
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
systime3.228
time3.42813396454
usrtime0.1
working_directory/project/teaser/genometeaser/tests_generated/e06f9a576d69697f7ad166f2c53eac4f

/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
memory283640000
return0
status1
stderr
None
stdout
88939 reads; of these:
88939 (100.00%) were paired; of these:
88079 (99.03%) aligned concordantly 0 times
173 (0.19%) aligned concordantly exactly 1 time
687 (0.77%) aligned concordantly >1 times
----
88079 pairs aligned concordantly 0 times; of these:
72732 (82.58%) aligned discordantly 1 time
----
15347 pairs aligned 0 times concordantly or discordantly; of these:
30694 mates make up the pairs; of these:
5 (0.02%) aligned 0 times
1588 (5.17%) aligned exactly 1 time
29101 (94.81%) aligned >1 times
100.00% overall alignment rate
systime8.568
time63.4552919865
usrtime216.208
working_directory/project/teaser/genometeaser/tests_generated/e06f9a576d69697f7ad166f2c53eac4f