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 Mapped50179995.972%
Wrongly Mapped206053.941%
Not Mapped4560.087%
Total522860100.0%
Read Failure Statistics
Not mapped4560.087%
Missing in mapper output00.0%
Mapped to wrong chromosome136432.609%
Mapped to wrong position69621.332%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments0
F-Measure0.979400
Precision0.960600
Recall0.999100
Timing
Raw Mapping Time212.968s
Effective Mapping Time209.176s
Effective Init Time3.792s
Effective Time MeasureCPU
Mapping Time (Wall)60.911s
Mapping Time (CPU)212.968s
Mapping Time (CPU User)205.008s
Mapping Time (CPU System)7.960s
Init Time (Wall)3.787s
Init Time (CPU)3.792s
Init Time (CPU User)0.144s
Init Time (CPU System)3.648s
Additional Information
Mapper Memory Usage3403 MB
Total Test Runtime (Wall)438.805s
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
memory3359372000
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
systime4.596
time289.416568041
usrtime0.112
working_directory/project/teaser/genometeaser/tests_generated/6a765d43cbdb960905eef4668388302e

/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
memory3358312000
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
systime3.648
time3.78746199608
usrtime0.144
working_directory/project/teaser/genometeaser/tests_generated/6a765d43cbdb960905eef4668388302e

/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
memory3403960000
return0
status1
stderr
None
stdout
261430 reads; of these:
261430 (100.00%) were paired; of these:
29099 (11.13%) aligned concordantly 0 times
197645 (75.60%) aligned concordantly exactly 1 time
34686 (13.27%) aligned concordantly >1 times
----
29099 pairs aligned concordantly 0 times; of these:
22438 (77.11%) aligned discordantly 1 time
----
6661 pairs aligned 0 times concordantly or discordantly; of these:
13322 mates make up the pairs; of these:
456 (3.42%) aligned 0 times
1210 (9.08%) aligned exactly 1 time
11656 (87.49%) aligned >1 times
99.91% overall alignment rate
systime7.96
time60.9111139774
usrtime205.008
working_directory/project/teaser/genometeaser/tests_generated/6a765d43cbdb960905eef4668388302e