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 Mapped17685488.673%
Wrongly Mapped25281.268%
Not Mapped2006410.06%
Total199446100.0%
Read Failure Statistics
Not mapped2006410.06%
Missing in mapper output00.0%
Mapped to wrong chromosome7810.392%
Mapped to wrong position17470.876%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments0
F-Measure0.940000
Precision0.985900
Recall0.898100
Timing
Raw Mapping Time139.528s
Effective Mapping Time135.916s
Effective Init Time3.612s
Effective Time MeasureCPU
Mapping Time (Wall)48.385s
Mapping Time (CPU)139.528s
Mapping Time (CPU User)132.628s
Mapping Time (CPU System)6.900s
Init Time (Wall)3.546s
Init Time (CPU)3.612s
Init Time (CPU User)0.132s
Init Time (CPU System)3.480s
Additional Information
Mapper Memory Usage229 MB
Total Test Runtime (Wall)135.240s
Mapper Command Line: 
/project/teaser/genometeaser/software/bowtie2/bowtie2 -p 4 -x /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas_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/Arabidopsis_thaliana.fas_bt -U reads_base.fastq -S out_bowtie2.sam

command/project/teaser/genometeaser/software/bowtie2/bowtie2 -p 4 -x /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas_bt -U reads_base.fastq -S out_bowtie2.sam
memory194768000
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
systime3.276
time14.4344220161
usrtime0.144
working_directory/project/teaser/genometeaser/tests_generated/ff62cbf4348f21949b4a4be50bea9679

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

command/project/teaser/genometeaser/software/bowtie2/bowtie2 -p 4 -x /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas_bt -U reads_base.fastq -S out_bowtie2.sam
memory194908000
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
systime3.48
time3.5461871624
usrtime0.132
working_directory/project/teaser/genometeaser/tests_generated/ff62cbf4348f21949b4a4be50bea9679

/project/teaser/genometeaser/software/bowtie2/bowtie2 -p 4 -x /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas_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/Arabidopsis_thaliana.fas_bt -1 reads1.fastq -2 reads2.fastq -S out_bowtie2.sam
memory229268000
return0
status1
stderr
None
stdout
99723 reads; of these:
99723 (100.00%) were paired; of these:
21806 (21.87%) aligned concordantly 0 times
72710 (72.91%) aligned concordantly exactly 1 time
5207 (5.22%) aligned concordantly >1 times
----
21806 pairs aligned concordantly 0 times; of these:
6971 (31.97%) aligned discordantly 1 time
----
14835 pairs aligned 0 times concordantly or discordantly; of these:
29670 mates make up the pairs; of these:
20064 (67.62%) aligned 0 times
7425 (25.03%) aligned exactly 1 time
2181 (7.35%) aligned >1 times
89.94% overall alignment rate
systime6.9
time48.385477066
usrtime132.628
working_directory/project/teaser/genometeaser/tests_generated/ff62cbf4348f21949b4a4be50bea9679