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 Mapped9928199.281%
Wrongly Mapped7190.719%
Not Mapped00.0%
Total100000100.0%
Read Failure Statistics
Not mapped00.0%
Missing in mapper output00.0%
Mapped to wrong chromosome4980.498%
Mapped to wrong position2210.221%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments0
F-Measure0.996400
Precision0.992800
Recall1.000000
Timing
Raw Mapping Time29.916s
Effective Mapping Time29.540s
Effective Init Time0.376s
Effective Time MeasureCPU
Mapping Time (Wall)11.489s
Mapping Time (CPU)29.916s
Mapping Time (CPU User)28.392s
Mapping Time (CPU System)1.524s
Init Time (Wall)0.356s
Init Time (CPU)0.376s
Init Time (CPU User)0.132s
Init Time (CPU System)0.244s
Additional Information
Mapper Memory Usage101 MB
Total Test Runtime (Wall)36.788s
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
memory71904000
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
systime0.288
time0.385459899902
usrtime0.124
working_directory/project/teaser/genometeaser/tests_generated/fea6b65881b1ab0892566fb478a26e05

/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
memory71312000
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
systime0.244
time0.355970859528
usrtime0.132
working_directory/project/teaser/genometeaser/tests_generated/fea6b65881b1ab0892566fb478a26e05

/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
memory101468000
return0
status1
stderr
None
stdout
50000 reads; of these:
50000 (100.00%) were paired; of these:
3023 (6.05%) aligned concordantly 0 times
45603 (91.21%) aligned concordantly exactly 1 time
1374 (2.75%) aligned concordantly >1 times
----
3023 pairs aligned concordantly 0 times; of these:
2908 (96.20%) aligned discordantly 1 time
----
115 pairs aligned 0 times concordantly or discordantly; of these:
230 mates make up the pairs; of these:
0 (0.00%) aligned 0 times
43 (18.70%) aligned exactly 1 time
187 (81.30%) aligned >1 times
100.00% overall alignment rate
systime1.524
time11.488754034
usrtime28.392
working_directory/project/teaser/genometeaser/tests_generated/fea6b65881b1ab0892566fb478a26e05