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 Mapped56858095.027%
Wrongly Mapped250054.179%
Not Mapped47530.794%
Total598338100.0%
Read Failure Statistics
Not mapped47530.794%
Missing in mapper output00.0%
Mapped to wrong chromosome122232.043%
Mapped to wrong position127822.136%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments0
F-Measure0.974500
Precision0.957900
Recall0.991700
Timing
Raw Mapping Time93.832s
Effective Mapping Time87.404s
Effective Init Time6.428s
Effective Time MeasureCPU
Mapping Time (Wall)38.144s
Mapping Time (CPU)93.832s
Mapping Time (CPU User)85.476s
Mapping Time (CPU System)8.356s
Init Time (Wall)6.512s
Init Time (CPU)6.428s
Init Time (CPU User)0.080s
Init Time (CPU System)6.348s
Additional Information
Mapper Memory Usage204 MB
Total Test Runtime (Wall)158.875s
Mapper Command Line: 
/project/teaser/genometeaser/software/bowtie2/bowtie2 -p 4 -x /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas_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/Arabidopsis_thaliana.fas_bt -U reads_base.fastq -S out_bowtie2.sam

command/project/teaser/genometeaser/software/bowtie2/bowtie2 -p 4 -x /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas_bt -U reads_base.fastq -S out_bowtie2.sam
memory194748000
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
systime5.352
time13.9115798473
usrtime0.116
working_directory/project/teaser/genometeaser/tests_generated/0542e1134664dca94011ee7ee39d31ff

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

command/project/teaser/genometeaser/software/bowtie2/bowtie2 -p 4 -x /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas_bt -U reads_base.fastq -S out_bowtie2.sam
memory194788000
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
systime6.348
time6.51205182076
usrtime0.08
working_directory/project/teaser/genometeaser/tests_generated/0542e1134664dca94011ee7ee39d31ff

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

command/project/teaser/genometeaser/software/bowtie2/bowtie2 -p 4 -x /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas_bt -U reads.fastq -S out_bowtie2.sam
memory204876000
return0
status1
stderr
None
stdout
598338 reads; of these:
598338 (100.00%) were unpaired; of these:
4753 (0.79%) aligned 0 times
503576 (84.16%) aligned exactly 1 time
90009 (15.04%) aligned >1 times
99.21% overall alignment rate
systime8.356
time38.1443870068
usrtime85.476
working_directory/project/teaser/genometeaser/tests_generated/0542e1134664dca94011ee7ee39d31ff