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 Mapped32492290.428%
Wrongly Mapped343659.564%
Not Mapped270.008%
Total359314100.0%
Read Failure Statistics
Not mapped270.008%
Missing in mapper output00.0%
Mapped to wrong chromosome187625.222%
Mapped to wrong position156034.342%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments0
F-Measure0.949700
Precision0.904400
Recall0.999900
Timing
Raw Mapping Time187.489s
Effective Mapping Time187.161s
Effective Init Time0.329s
Effective Time MeasureCPU
Mapping Time (Wall)48.471s
Mapping Time (CPU)187.489s
Mapping Time (CPU User)183.660s
Mapping Time (CPU System)3.829s
Init Time (Wall)0.321s
Init Time (CPU)0.329s
Init Time (CPU User)0.080s
Init Time (CPU System)0.249s
Additional Information
Mapper Memory Usage256 MB
Total Test Runtime (Wall)76.102s
Mapper Command Line: 
/project/teaser/genometeaser/software/bowtie2/bowtie2 -p 4 -x /project/teaser/genometeaser/references/D_melanogaster.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/D_melanogaster.fasta_bt -U reads_base.fastq -S out_bowtie2.sam

command/project/teaser/genometeaser/software/bowtie2/bowtie2 -p 4 -x /project/teaser/genometeaser/references/D_melanogaster.fasta_bt -U reads_base.fastq -S out_bowtie2.sam
memory209684000
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
systime0.236963
time0.309201955795
usrtime0.085986
working_directory/project/teaser/genometeaser/tests_generated/6e77d132a218d55fc27515c6d7f3e63e

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

command/project/teaser/genometeaser/software/bowtie2/bowtie2 -p 4 -x /project/teaser/genometeaser/references/D_melanogaster.fasta_bt -U reads_base.fastq -S out_bowtie2.sam
memory208892000
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
systime0.248962
time0.321497917175
usrtime0.079987
working_directory/project/teaser/genometeaser/tests_generated/6e77d132a218d55fc27515c6d7f3e63e

/project/teaser/genometeaser/software/bowtie2/bowtie2 -p 4 -x /project/teaser/genometeaser/references/D_melanogaster.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/D_melanogaster.fasta_bt -1 reads1.fastq -2 reads2.fastq -S out_bowtie2.sam
memory256164000
return0
status1
stderr
None
stdout
179657 reads; of these:
179657 (100.00%) were paired; of these:
87854 (48.90%) aligned concordantly 0 times
74839 (41.66%) aligned concordantly exactly 1 time
16964 (9.44%) aligned concordantly >1 times
----
87854 pairs aligned concordantly 0 times; of these:
72605 (82.64%) aligned discordantly 1 time
----
15249 pairs aligned 0 times concordantly or discordantly; of these:
30498 mates make up the pairs; of these:
27 (0.09%) aligned 0 times
783 (2.57%) aligned exactly 1 time
29688 (97.34%) aligned >1 times
99.99% overall alignment rate
systime3.829417
time48.4707551003
usrtime183.660079
working_directory/project/teaser/genometeaser/tests_generated/6e77d132a218d55fc27515c6d7f3e63e