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 Mapped29459793.907%
Wrongly Mapped163065.198%
Not Mapped28100.896%
Total313713100.0%
Read Failure Statistics
Not mapped28100.896%
Missing in mapper output00.0%
Mapped to wrong chromosome123183.927%
Mapped to wrong position39881.271%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment3
Secondary Alignments0
F-Measure0.968600
Precision0.947600
Recall0.990600
Timing
Raw Mapping Time25.626s
Effective Mapping Time24.866s
Effective Init Time0.760s
Effective Time MeasureWall clock
Mapping Time (Wall)25.626s
Mapping Time (CPU)94.972s
Mapping Time (CPU User)93.916s
Mapping Time (CPU System)1.056s
Init Time (Wall)0.760s
Init Time (CPU)0.744s
Init Time (CPU User)0.039s
Init Time (CPU System)0.705s
Additional Information
Mapper Memory Usage3384 MB
Total Test Runtime (Wall)41.187s
Mapper Command Line: 
/project2/NextGenMapTest/Teaser/software/bowtie2/bowtie2 -p 4 -x /project2/NextGenMapTest/Teaser/references/GRCh37.fa_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/GRCh37.fa_bt -U reads_base.fastq -S out_bowtie2.sam

command/project2/NextGenMapTest/Teaser/software/bowtie2/bowtie2 -p 4 -x /project2/NextGenMapTest/Teaser/references/GRCh37.fa_bt -U reads_base.fastq -S out_bowtie2.sam
memory3357212000
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
systime0.707892
time0.717758893967
usrtime0.038994
working_directory/project2/NextGenMapTest/Teaser/tests_generated/H2_n

/project2/NextGenMapTest/Teaser/software/bowtie2/bowtie2 -p 4 -x /project2/NextGenMapTest/Teaser/references/GRCh37.fa_bt -U reads_base.fastq -S out_bowtie2.sam

command/project2/NextGenMapTest/Teaser/software/bowtie2/bowtie2 -p 4 -x /project2/NextGenMapTest/Teaser/references/GRCh37.fa_bt -U reads_base.fastq -S out_bowtie2.sam
memory3357148000
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
systime0.704892
time0.7596180439
usrtime0.038994
working_directory/project2/NextGenMapTest/Teaser/tests_generated/H2_n

/project2/NextGenMapTest/Teaser/software/bowtie2/bowtie2 -p 4 -x /project2/NextGenMapTest/Teaser/references/GRCh37.fa_bt -U reads.fastq -S out_bowtie2.sam

command/project2/NextGenMapTest/Teaser/software/bowtie2/bowtie2 -p 4 -x /project2/NextGenMapTest/Teaser/references/GRCh37.fa_bt -U reads.fastq -S out_bowtie2.sam
memory3384264000
return0
status1
stderr

None
stdout

313716 reads; of these:

  313716 (100.00%) were unpaired; of these:

    2811 (0.90%) aligned 0 times

    241809 (77.08%) aligned exactly 1 time

    69096 (22.03%) aligned >1 times

99.10% overall alignment rate
systime1.055839
time25.6255431175
usrtime93.915722
working_directory/project2/NextGenMapTest/Teaser/tests_generated/H2_n