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 Mapped82677094.875%
Wrongly Mapped411664.724%
Not Mapped34960.401%
Total871432100.0%
Read Failure Statistics
Not mapped34960.401%
Missing in mapper output00.0%
Mapped to wrong chromosome287433.298%
Mapped to wrong position124231.426%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments0
F-Measure0.973700
Precision0.952600
Recall0.995800
Timing
Raw Mapping Time312.056s
Effective Mapping Time308.372s
Effective Init Time3.684s
Effective Time MeasureCPU
Mapping Time (Wall)81.951s
Mapping Time (CPU)312.056s
Mapping Time (CPU User)304.792s
Mapping Time (CPU System)7.264s
Init Time (Wall)3.688s
Init Time (CPU)3.684s
Init Time (CPU User)0.108s
Init Time (CPU System)3.576s
Additional Information
Mapper Memory Usage3393 MB
Total Test Runtime (Wall)449.254s
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
memory3361560000
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
systime4.444
time289.291460991
usrtime0.1
working_directory/project/teaser/genometeaser/tests_generated/ab0014cf05e86cd590ae0b3283410abf

/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
memory3360448000
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
systime3.576
time3.68810415268
usrtime0.108
working_directory/project/teaser/genometeaser/tests_generated/ab0014cf05e86cd590ae0b3283410abf

/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
memory3393964000
return0
status1
stderr
None
stdout
435716 reads; of these:
435716 (100.00%) were paired; of these:
2790 (0.64%) aligned concordantly 0 times
374139 (85.87%) aligned concordantly exactly 1 time
58787 (13.49%) aligned concordantly >1 times
----
2790 pairs aligned concordantly 0 times; of these:
1 (0.04%) aligned discordantly 1 time
----
2789 pairs aligned 0 times concordantly or discordantly; of these:
5578 mates make up the pairs; of these:
3496 (62.67%) aligned 0 times
240 (4.30%) aligned exactly 1 time
1842 (33.02%) aligned >1 times
99.60% overall alignment rate
systime7.264
time81.9506950378
usrtime304.792
working_directory/project/teaser/genometeaser/tests_generated/ab0014cf05e86cd590ae0b3283410abf