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 Mapped9906399.063%
Wrongly Mapped7060.706%
Not Mapped2310.231%
Total100000100.0%
Read Failure Statistics
Not mapped2310.231%
Missing in mapper output00.0%
Mapped to wrong chromosome4940.494%
Mapped to wrong position2120.212%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments0
F-Measure0.995300
Precision0.992900
Recall0.997700
Timing
Raw Mapping Time31.500s
Effective Mapping Time31.100s
Effective Init Time0.400s
Effective Time MeasureCPU
Mapping Time (Wall)11.945s
Mapping Time (CPU)31.500s
Mapping Time (CPU User)30.276s
Mapping Time (CPU System)1.224s
Init Time (Wall)0.348s
Init Time (CPU)0.400s
Init Time (CPU User)0.140s
Init Time (CPU System)0.260s
Additional Information
Mapper Memory Usage101 MB
Total Test Runtime (Wall)39.588s
Mapper Command Line: 
/project/teaser/genometeaser/software/bowtie2/bowtie2 -p 4 -x /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.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/Saccharomyces_cerevisiae.fasta_bt -U reads_base.fastq -S out_bowtie2.sam

command/project/teaser/genometeaser/software/bowtie2/bowtie2 -p 4 -x /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta_bt -U reads_base.fastq -S out_bowtie2.sam
memory73800000
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
systime0.292
time0.370971918106
usrtime0.128
working_directory/project/teaser/genometeaser/tests_generated/bc5e667ff41f75be5690d71ac8911c05

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

command/project/teaser/genometeaser/software/bowtie2/bowtie2 -p 4 -x /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta_bt -U reads_base.fastq -S out_bowtie2.sam
memory71948000
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
systime0.26
time0.348499059677
usrtime0.14
working_directory/project/teaser/genometeaser/tests_generated/bc5e667ff41f75be5690d71ac8911c05

/project/teaser/genometeaser/software/bowtie2/bowtie2 -p 4 -x /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.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/Saccharomyces_cerevisiae.fasta_bt -1 reads1.fastq -2 reads2.fastq -S out_bowtie2.sam
memory101300000
return0
status1
stderr
None
stdout
50000 reads; of these:
50000 (100.00%) were paired; of these:
179 (0.36%) aligned concordantly 0 times
48485 (96.97%) aligned concordantly exactly 1 time
1336 (2.67%) aligned concordantly >1 times
----
179 pairs aligned concordantly 0 times; of these:
59 (32.96%) aligned discordantly 1 time
----
120 pairs aligned 0 times concordantly or discordantly; of these:
240 mates make up the pairs; of these:
231 (96.25%) aligned 0 times
7 (2.92%) aligned exactly 1 time
2 (0.83%) aligned >1 times
99.77% overall alignment rate
systime1.224
time11.9448559284
usrtime30.276
working_directory/project/teaser/genometeaser/tests_generated/bc5e667ff41f75be5690d71ac8911c05