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 Mapped64887190.293%
Wrongly Mapped688039.574%
Not Mapped9540.133%
Total718628100.0%
Read Failure Statistics
Not mapped9540.133%
Missing in mapper output00.0%
Mapped to wrong chromosome378905.273%
Mapped to wrong position309134.302%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments0
F-Measure0.949000
Precision0.904100
Recall0.998500
Timing
Raw Mapping Time168.396s
Effective Mapping Time167.824s
Effective Init Time0.572s
Effective Time MeasureCPU
Mapping Time (Wall)49.393s
Mapping Time (CPU)168.396s
Mapping Time (CPU User)165.856s
Mapping Time (CPU System)2.540s
Init Time (Wall)0.570s
Init Time (CPU)0.572s
Init Time (CPU User)0.188s
Init Time (CPU System)0.384s
Additional Information
Mapper Memory Usage248 MB
Total Test Runtime (Wall)170.914s
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
memory221520000
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
systime0.412
time0.563056945801
usrtime0.152
working_directory/project/teaser/genometeaser/tests_generated/e36fcf554e99e1f3a2b5fd499196eaa6

/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
memory224100000
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
systime0.384
time0.57036614418
usrtime0.188
working_directory/project/teaser/genometeaser/tests_generated/e36fcf554e99e1f3a2b5fd499196eaa6

/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
memory248120000
return0
status1
stderr
None
stdout
359314 reads; of these:
359314 (100.00%) were paired; of these:
3252 (0.91%) aligned concordantly 0 times
296012 (82.38%) aligned concordantly exactly 1 time
60050 (16.71%) aligned concordantly >1 times
----
3252 pairs aligned concordantly 0 times; of these:
2276 (69.99%) aligned discordantly 1 time
----
976 pairs aligned 0 times concordantly or discordantly; of these:
1952 mates make up the pairs; of these:
954 (48.87%) aligned 0 times
32 (1.64%) aligned exactly 1 time
966 (49.49%) aligned >1 times
99.87% overall alignment rate
systime2.54
time49.3926990032
usrtime165.856
working_directory/project/teaser/genometeaser/tests_generated/e36fcf554e99e1f3a2b5fd499196eaa6