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 Mapped50181695.975%
Wrongly Mapped205973.939%
Not Mapped4470.085%
Total522860100.0%
Read Failure Statistics
Not mapped4470.085%
Missing in mapper output00.0%
Mapped to wrong chromosome139722.672%
Mapped to wrong position66251.267%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments0
F-Measure0.979500
Precision0.960600
Recall0.999100
Timing
Raw Mapping Time196.928s
Effective Mapping Time192.232s
Effective Init Time4.696s
Effective Time MeasureCPU
Mapping Time (Wall)55.554s
Mapping Time (CPU)196.928s
Mapping Time (CPU User)190.080s
Mapping Time (CPU System)6.848s
Init Time (Wall)4.619s
Init Time (CPU)4.696s
Init Time (CPU User)0.136s
Init Time (CPU System)4.560s
Additional Information
Mapper Memory Usage3402 MB
Total Test Runtime (Wall)437.797s
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
memory3359516000
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
systime6.764
time289.286568165
usrtime0.16
working_directory/project/teaser/genometeaser/tests_generated/24d206dec9772782e6efab15944abfc6

/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
memory3359368000
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
systime4.56
time4.61929106712
usrtime0.136
working_directory/project/teaser/genometeaser/tests_generated/24d206dec9772782e6efab15944abfc6

/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
memory3402892000
return0
status1
stderr
None
stdout
261430 reads; of these:
261430 (100.00%) were paired; of these:
29277 (11.20%) aligned concordantly 0 times
197085 (75.39%) aligned concordantly exactly 1 time
35068 (13.41%) aligned concordantly >1 times
----
29277 pairs aligned concordantly 0 times; of these:
22695 (77.52%) aligned discordantly 1 time
----
6582 pairs aligned 0 times concordantly or discordantly; of these:
13164 mates make up the pairs; of these:
447 (3.40%) aligned 0 times
1199 (9.11%) aligned exactly 1 time
11518 (87.50%) aligned >1 times
99.91% overall alignment rate
systime6.848
time55.5540709496
usrtime190.08
working_directory/project/teaser/genometeaser/tests_generated/24d206dec9772782e6efab15944abfc6