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 Mapped40389796.56%
Wrongly Mapped139583.337%
Not Mapped4330.104%
Total418288100.0%
Read Failure Statistics
Not mapped4330.104%
Missing in mapper output00.0%
Mapped to wrong chromosome88052.105%
Mapped to wrong position51531.232%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments0
F-Measure0.982500
Precision0.966600
Recall0.998900
Timing
Raw Mapping Time271.616s
Effective Mapping Time211.068s
Effective Init Time60.548s
Effective Time MeasureCPU
Mapping Time (Wall)116.638s
Mapping Time (CPU)271.616s
Mapping Time (CPU User)187.812s
Mapping Time (CPU System)83.804s
Init Time (Wall)61.216s
Init Time (CPU)60.548s
Init Time (CPU User)0.096s
Init Time (CPU System)60.452s
Additional Information
Mapper Memory Usage3404 MB
Total Test Runtime (Wall)545.615s
Mapper Command Line: 
/project/teaser/genometeaser/software/bowtie2/bowtie2 -p 4 -x /project/teaser/genometeaser/references/H_sapiens.fa_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/H_sapiens.fa_bt -U reads_base.fastq -S out_bowtie2.sam

command/project/teaser/genometeaser/software/bowtie2/bowtie2 -p 4 -x /project/teaser/genometeaser/references/H_sapiens.fa_bt -U reads_base.fastq -S out_bowtie2.sam
memory3359644000
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
systime57.912
time290.39136219
usrtime0.104
working_directory/project/teaser/genometeaser/tests_generated/a5e600139d12b867a2e96eee861838f1

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

command/project/teaser/genometeaser/software/bowtie2/bowtie2 -p 4 -x /project/teaser/genometeaser/references/H_sapiens.fa_bt -U reads_base.fastq -S out_bowtie2.sam
memory3359640000
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
systime60.452
time61.2156631947
usrtime0.096
working_directory/project/teaser/genometeaser/tests_generated/a5e600139d12b867a2e96eee861838f1

/project/teaser/genometeaser/software/bowtie2/bowtie2 -p 4 -x /project/teaser/genometeaser/references/H_sapiens.fa_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/H_sapiens.fa_bt -1 reads1.fastq -2 reads2.fastq -S out_bowtie2.sam
memory3404944000
return0
status1
stderr
None
stdout
209144 reads; of these:
209144 (100.00%) were paired; of these:
44879 (21.46%) aligned concordantly 0 times
147136 (70.35%) aligned concordantly exactly 1 time
17129 (8.19%) aligned concordantly >1 times
----
44879 pairs aligned concordantly 0 times; of these:
33885 (75.50%) aligned discordantly 1 time
----
10994 pairs aligned 0 times concordantly or discordantly; of these:
21988 mates make up the pairs; of these:
433 (1.97%) aligned 0 times
6464 (29.40%) aligned exactly 1 time
15091 (68.63%) aligned >1 times
99.90% overall alignment rate
systime83.804
time116.637727022
usrtime187.812
working_directory/project/teaser/genometeaser/tests_generated/a5e600139d12b867a2e96eee861838f1