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 Mapped22299696.632%
Wrongly Mapped76543.317%
Not Mapped1180.051%
Total230768100.0%
Read Failure Statistics
Not mapped1180.051%
Missing in mapper output00.0%
Mapped to wrong chromosome00.0%
Mapped to wrong position76543.317%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments0
F-Measure0.982900
Precision0.966800
Recall0.999500
Timing
Raw Mapping Time73.848s
Effective Mapping Time73.232s
Effective Init Time0.616s
Effective Time MeasureCPU
Mapping Time (Wall)32.773s
Mapping Time (CPU)73.848s
Mapping Time (CPU User)70.488s
Mapping Time (CPU System)3.360s
Init Time (Wall)0.638s
Init Time (CPU)0.616s
Init Time (CPU User)0.108s
Init Time (CPU System)0.508s
Additional Information
Mapper Memory Usage82 MB
Total Test Runtime (Wall)87.760s
Mapper Command Line: 
/project/teaser/genometeaser/software/bowtie2/bowtie2 -p 4 -x /project/teaser/genometeaser/references/E_coli.fasta_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/E_coli.fasta_bt -U reads_base.fastq -S out_bowtie2.sam

command/project/teaser/genometeaser/software/bowtie2/bowtie2 -p 4 -x /project/teaser/genometeaser/references/E_coli.fasta_bt -U reads_base.fastq -S out_bowtie2.sam
memory56164000
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
systime0.384
time2.92858576775
usrtime0.084
working_directory/project/teaser/genometeaser/tests_generated/f3cfc70a77888b8626def783d24d0e80

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

command/project/teaser/genometeaser/software/bowtie2/bowtie2 -p 4 -x /project/teaser/genometeaser/references/E_coli.fasta_bt -U reads_base.fastq -S out_bowtie2.sam
memory63708000
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
systime0.508
time0.637941837311
usrtime0.108
working_directory/project/teaser/genometeaser/tests_generated/f3cfc70a77888b8626def783d24d0e80

/project/teaser/genometeaser/software/bowtie2/bowtie2 -p 4 -x /project/teaser/genometeaser/references/E_coli.fasta_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/E_coli.fasta_bt -1 reads1.fastq -2 reads2.fastq -S out_bowtie2.sam
memory82356000
return0
status1
stderr
None
stdout
115384 reads; of these:
115384 (100.00%) were paired; of these:
625 (0.54%) aligned concordantly 0 times
108138 (93.72%) aligned concordantly exactly 1 time
6621 (5.74%) aligned concordantly >1 times
----
625 pairs aligned concordantly 0 times; of these:
535 (85.60%) aligned discordantly 1 time
----
90 pairs aligned 0 times concordantly or discordantly; of these:
180 mates make up the pairs; of these:
118 (65.56%) aligned 0 times
4 (2.22%) aligned exactly 1 time
58 (32.22%) aligned >1 times
99.95% overall alignment rate
systime3.36
time32.7733659744
usrtime70.488
working_directory/project/teaser/genometeaser/tests_generated/f3cfc70a77888b8626def783d24d0e80