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 Mapped73948194.287%
Wrongly Mapped417155.319%
Not Mapped30940.394%
Total784290100.0%
Read Failure Statistics
Not mapped30940.394%
Missing in mapper output00.0%
Mapped to wrong chromosome296493.78%
Mapped to wrong position120661.538%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments0
F-Measure0.970600
Precision0.946600
Recall0.995800
Timing
Raw Mapping Time222.228s
Effective Mapping Time218.156s
Effective Init Time4.072s
Effective Time MeasureCPU
Mapping Time (Wall)64.494s
Mapping Time (CPU)222.228s
Mapping Time (CPU User)215.560s
Mapping Time (CPU System)6.668s
Init Time (Wall)4.042s
Init Time (CPU)4.072s
Init Time (CPU User)0.136s
Init Time (CPU System)3.936s
Additional Information
Mapper Memory Usage3395 MB
Total Test Runtime (Wall)456.854s
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
memory3359308000
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
systime6.36
time289.777333975
usrtime0.1
working_directory/project/teaser/genometeaser/tests_generated/959fff07f73e2ad276591caaff4e83fa

/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
memory3359368000
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
systime3.936
time4.04248785973
usrtime0.136
working_directory/project/teaser/genometeaser/tests_generated/959fff07f73e2ad276591caaff4e83fa

/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
memory3395620000
return0
status1
stderr
None
stdout
392145 reads; of these:
392145 (100.00%) were paired; of these:
15236 (3.89%) aligned concordantly 0 times
316572 (80.73%) aligned concordantly exactly 1 time
60337 (15.39%) aligned concordantly >1 times
----
15236 pairs aligned concordantly 0 times; of these:
10048 (65.95%) aligned discordantly 1 time
----
5188 pairs aligned 0 times concordantly or discordantly; of these:
10376 mates make up the pairs; of these:
3094 (29.82%) aligned 0 times
679 (6.54%) aligned exactly 1 time
6603 (63.64%) aligned >1 times
99.61% overall alignment rate
systime6.668
time64.4940760136
usrtime215.56
working_directory/project/teaser/genometeaser/tests_generated/959fff07f73e2ad276591caaff4e83fa