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 Mapped54506891.018%
Wrongly Mapped534298.922%
Not Mapped3610.06%
Total598858100.0%
Read Failure Statistics
Not mapped3610.06%
Missing in mapper output00.0%
Mapped to wrong chromosome287144.795%
Mapped to wrong position247154.127%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments0
F-Measure0.953000
Precision0.910700
Recall0.999300
Timing
Raw Mapping Time220.804s
Effective Mapping Time216.172s
Effective Init Time4.632s
Effective Time MeasureCPU
Mapping Time (Wall)64.320s
Mapping Time (CPU)220.804s
Mapping Time (CPU User)209.672s
Mapping Time (CPU System)11.132s
Init Time (Wall)4.682s
Init Time (CPU)4.632s
Init Time (CPU User)0.140s
Init Time (CPU System)4.492s
Additional Information
Mapper Memory Usage250 MB
Total Test Runtime (Wall)174.589s
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
memory220856000
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
systime4.176
time16.2706201077
usrtime0.144
working_directory/project/teaser/genometeaser/tests_generated/b705aa0185e37b61d45ed27cf2a0ba62

/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
memory220572000
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
systime4.492
time4.68164086342
usrtime0.14
working_directory/project/teaser/genometeaser/tests_generated/b705aa0185e37b61d45ed27cf2a0ba62

/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
memory250308000
return0
status1
stderr
None
stdout
299429 reads; of these:
299429 (100.00%) were paired; of these:
1126 (0.38%) aligned concordantly 0 times
248838 (83.10%) aligned concordantly exactly 1 time
49465 (16.52%) aligned concordantly >1 times
----
1126 pairs aligned concordantly 0 times; of these:
756 (67.14%) aligned discordantly 1 time
----
370 pairs aligned 0 times concordantly or discordantly; of these:
740 mates make up the pairs; of these:
361 (48.78%) aligned 0 times
6 (0.81%) aligned exactly 1 time
373 (50.41%) aligned >1 times
99.94% overall alignment rate
systime11.132
time64.3195919991
usrtime209.672
working_directory/project/teaser/genometeaser/tests_generated/b705aa0185e37b61d45ed27cf2a0ba62