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 Mapped50090995.802%
Wrongly Mapped215154.115%
Not Mapped4360.083%
Total522860100.0%
Read Failure Statistics
Not mapped4360.083%
Missing in mapper output00.0%
Mapped to wrong chromosome143182.738%
Mapped to wrong position71971.376%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments0
F-Measure0.978600
Precision0.958800
Recall0.999100
Timing
Raw Mapping Time150.140s
Effective Mapping Time146.292s
Effective Init Time3.848s
Effective Time MeasureCPU
Mapping Time (Wall)46.261s
Mapping Time (CPU)150.140s
Mapping Time (CPU User)143.400s
Mapping Time (CPU System)6.740s
Init Time (Wall)3.838s
Init Time (CPU)3.848s
Init Time (CPU User)0.116s
Init Time (CPU System)3.732s
Additional Information
Mapper Memory Usage3403 MB
Total Test Runtime (Wall)431.032s
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
memory3359524000
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
systime4.644
time289.560949802
usrtime0.132
working_directory/project/teaser/genometeaser/tests_generated/293e14569a4a233bf507f46e325e460e

/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
memory3359532000
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
systime3.732
time3.83806610107
usrtime0.116
working_directory/project/teaser/genometeaser/tests_generated/293e14569a4a233bf507f46e325e460e

/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
memory3403040000
return0
status1
stderr
None
stdout
261430 reads; of these:
261430 (100.00%) were paired; of these:
29054 (11.11%) aligned concordantly 0 times
197094 (75.39%) aligned concordantly exactly 1 time
35282 (13.50%) aligned concordantly >1 times
----
29054 pairs aligned concordantly 0 times; of these:
22377 (77.02%) aligned discordantly 1 time
----
6677 pairs aligned 0 times concordantly or discordantly; of these:
13354 mates make up the pairs; of these:
436 (3.26%) aligned 0 times
1165 (8.72%) aligned exactly 1 time
11753 (88.01%) aligned >1 times
99.92% overall alignment rate
systime6.74
time46.2607281208
usrtime143.4
working_directory/project/teaser/genometeaser/tests_generated/293e14569a4a233bf507f46e325e460e