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 Mapped58890295.736%
Wrongly Mapped252384.103%
Not Mapped9880.161%
Total615128100.0%
Read Failure Statistics
Not mapped9880.161%
Missing in mapper output00.0%
Mapped to wrong chromosome176132.863%
Mapped to wrong position76251.24%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments0
F-Measure0.978200
Precision0.958900
Recall0.998300
Timing
Raw Mapping Time336.408s
Effective Mapping Time303.096s
Effective Init Time33.312s
Effective Time MeasureCPU
Mapping Time (Wall)135.573s
Mapping Time (CPU)336.408s
Mapping Time (CPU User)275.864s
Mapping Time (CPU System)60.544s
Init Time (Wall)37.304s
Init Time (CPU)33.312s
Init Time (CPU User)0.136s
Init Time (CPU System)33.176s
Additional Information
Mapper Memory Usage3398 MB
Total Test Runtime (Wall)666.303s
Mapper Command Line: 
/project/teaser/genometeaser/software/bowtie2/bowtie2 -p 4 -x /project/teaser/genometeaser/references/H_sapiens.fa_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/H_sapiens.fa_bt -U reads_base.fastq -S out_bowtie2.sam

command/project/teaser/genometeaser/software/bowtie2/bowtie2 -p 4 -x /project/teaser/genometeaser/references/H_sapiens.fa_bt -U reads_base.fastq -S out_bowtie2.sam
memory3354808000
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
systime34.392
time374.690731049
usrtime0.192
working_directory/project/teaser/genometeaser/tests_generated/4ff0769a44d529563c64b75a1aaf552d

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

command/project/teaser/genometeaser/software/bowtie2/bowtie2 -p 4 -x /project/teaser/genometeaser/references/H_sapiens.fa_bt -U reads_base.fastq -S out_bowtie2.sam
memory3358608000
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
systime33.176
time37.3037369251
usrtime0.136
working_directory/project/teaser/genometeaser/tests_generated/4ff0769a44d529563c64b75a1aaf552d

/project/teaser/genometeaser/software/bowtie2/bowtie2 -p 4 -x /project/teaser/genometeaser/references/H_sapiens.fa_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/H_sapiens.fa_bt -1 reads1.fastq -2 reads2.fastq -S out_bowtie2.sam
memory3398980000
return0
status1
stderr
None
stdout
307564 reads; of these:
307564 (100.00%) were paired; of these:
21109 (6.86%) aligned concordantly 0 times
243808 (79.27%) aligned concordantly exactly 1 time
42647 (13.87%) aligned concordantly >1 times
----
21109 pairs aligned concordantly 0 times; of these:
15845 (75.06%) aligned discordantly 1 time
----
5264 pairs aligned 0 times concordantly or discordantly; of these:
10528 mates make up the pairs; of these:
988 (9.38%) aligned 0 times
893 (8.48%) aligned exactly 1 time
8647 (82.13%) aligned >1 times
99.84% overall alignment rate
systime60.544
time135.572632074
usrtime275.864
working_directory/project/teaser/genometeaser/tests_generated/4ff0769a44d529563c64b75a1aaf552d