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 Mapped131562580.553%
Wrongly Mapped24654215.095%
Not Mapped710824.352%
Total1633249100.0%
Read Failure Statistics
Not mapped710824.352%
Missing in mapper output00.0%
Mapped to wrong chromosome16569710.145%
Mapped to wrong position808354.949%
Mapped to wrong strand100.001%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments0
F-Measure0.892300
Precision0.842200
Recall0.948700
Timing
Raw Mapping Time19.661s
Effective Mapping Time19.423s
Effective Init Time0.238s
Effective Time MeasureWall clock
Mapping Time (Wall)19.661s
Mapping Time (CPU)67.459s
Mapping Time (CPU User)66.534s
Mapping Time (CPU System)0.925s
Init Time (Wall)0.238s
Init Time (CPU)0.216s
Init Time (CPU User)0.058s
Init Time (CPU System)0.158s
Additional Information
Mapper Memory Usage227 MB
Total Test Runtime (Wall)78.182s
Mapper Command Line: 
/project2/NextGenMapTest/Teaser/software/bowtie2/bowtie2 -p 4 -x /project2/NextGenMapTest/Teaser/references/d_melanogaster.fasta_bt -U reads.fastq -S out_bowtie2.sam
Errors and Warnings
No problems were encountered.
Subprocess Log

/project2/NextGenMapTest/Teaser/software/bowtie2/bowtie2 -p 4 -x /project2/NextGenMapTest/Teaser/references/d_melanogaster.fasta_bt -U reads_base.fastq -S out_bowtie2.sam

command/project2/NextGenMapTest/Teaser/software/bowtie2/bowtie2 -p 4 -x /project2/NextGenMapTest/Teaser/references/d_melanogaster.fasta_bt -U reads_base.fastq -S out_bowtie2.sam
memory224280000
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
systime0.158975
time0.172477960587
usrtime0.054991
working_directory/project2/NextGenMapTest/Teaser/tests_generated/D4_n

/project2/NextGenMapTest/Teaser/software/bowtie2/bowtie2 -p 4 -x /project2/NextGenMapTest/Teaser/references/d_melanogaster.fasta_bt -U reads_base.fastq -S out_bowtie2.sam

command/project2/NextGenMapTest/Teaser/software/bowtie2/bowtie2 -p 4 -x /project2/NextGenMapTest/Teaser/references/d_melanogaster.fasta_bt -U reads_base.fastq -S out_bowtie2.sam
memory219860000
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
systime0.157975
time0.237946987152
usrtime0.057991
working_directory/project2/NextGenMapTest/Teaser/tests_generated/D4_n

/project2/NextGenMapTest/Teaser/software/bowtie2/bowtie2 -p 4 -x /project2/NextGenMapTest/Teaser/references/d_melanogaster.fasta_bt -U reads.fastq -S out_bowtie2.sam

command/project2/NextGenMapTest/Teaser/software/bowtie2/bowtie2 -p 4 -x /project2/NextGenMapTest/Teaser/references/d_melanogaster.fasta_bt -U reads.fastq -S out_bowtie2.sam
memory227840000
return0
status1
stderr

None
stdout

1633249 reads; of these:

  1633249 (100.00%) were unpaired; of these:

    71082 (4.35%) aligned 0 times

    1221432 (74.79%) aligned exactly 1 time

    340735 (20.86%) aligned >1 times

95.65% overall alignment rate
systime0.924859
time19.6609270573
usrtime66.533885
working_directory/project2/NextGenMapTest/Teaser/tests_generated/D4_n