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 Mapped161122773.261%
Wrongly Mapped50873023.132%
Not Mapped793273.607%
Total2199284100.0%
Read Failure Statistics
Not mapped793273.607%
Missing in mapper output00.0%
Mapped to wrong chromosome38700717.597%
Mapped to wrong position1217185.534%
Mapped to wrong strand50.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments0
F-Measure0.845700
Precision0.760000
Recall0.953100
Timing
Raw Mapping Time349.332s
Effective Mapping Time345.840s
Effective Init Time3.492s
Effective Time MeasureCPU
Mapping Time (Wall)97.349s
Mapping Time (CPU)349.332s
Mapping Time (CPU User)341.352s
Mapping Time (CPU System)7.980s
Init Time (Wall)3.460s
Init Time (CPU)3.492s
Init Time (CPU User)0.108s
Init Time (CPU System)3.384s
Additional Information
Mapper Memory Usage3097 MB
Total Test Runtime (Wall)710.157s
Mapper Command Line: 
/project/teaser/genometeaser/software/bowtie2/bowtie2 -p 4 -x /project/teaser/genometeaser/references/M_musculus.fasta_bt -U reads.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/M_musculus.fasta_bt -U reads_base.fastq -S out_bowtie2.sam

command/project/teaser/genometeaser/software/bowtie2/bowtie2 -p 4 -x /project/teaser/genometeaser/references/M_musculus.fasta_bt -U reads_base.fastq -S out_bowtie2.sam
memory3088176000
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
systime4.272
time265.290751934
usrtime0.116
working_directory/project/teaser/genometeaser/tests_generated/3f55d5f326042c6d121b7048b0ae8ccd

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

command/project/teaser/genometeaser/software/bowtie2/bowtie2 -p 4 -x /project/teaser/genometeaser/references/M_musculus.fasta_bt -U reads_base.fastq -S out_bowtie2.sam
memory3088164000
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
systime3.384
time3.46028709412
usrtime0.108
working_directory/project/teaser/genometeaser/tests_generated/3f55d5f326042c6d121b7048b0ae8ccd

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

command/project/teaser/genometeaser/software/bowtie2/bowtie2 -p 4 -x /project/teaser/genometeaser/references/M_musculus.fasta_bt -U reads.fastq -S out_bowtie2.sam
memory3097932000
return0
status1
stderr
None
stdout
2199284 reads; of these:
2199284 (100.00%) were unpaired; of these:
79327 (3.61%) aligned 0 times
1289260 (58.62%) aligned exactly 1 time
830697 (37.77%) aligned >1 times
96.39% overall alignment rate
systime7.98
time97.3494031429
usrtime341.352
working_directory/project/teaser/genometeaser/tests_generated/3f55d5f326042c6d121b7048b0ae8ccd