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 Mapped20296484.73%
Wrongly Mapped192328.029%
Not Mapped173477.242%
Total239543100.0%
Read Failure Statistics
Not mapped173477.242%
Missing in mapper output00.0%
Mapped to wrong chromosome107844.502%
Mapped to wrong position84483.527%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments0
F-Measure0.917300
Precision0.913400
Recall0.921300
Timing
Raw Mapping Time13.851s
Effective Mapping Time13.585s
Effective Init Time0.266s
Effective Time MeasureWall clock
Mapping Time (Wall)13.851s
Mapping Time (CPU)50.228s
Mapping Time (CPU User)49.719s
Mapping Time (CPU System)0.509s
Init Time (Wall)0.266s
Init Time (CPU)0.176s
Init Time (CPU User)0.052s
Init Time (CPU System)0.124s
Additional Information
Mapper Memory Usage238 MB
Total Test Runtime (Wall)33.811s
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
memory219868000
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
systime0.136979
time0.160205125809
usrtime0.055991
working_directory/project2/NextGenMapTest/Teaser/tests_generated/D2_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
memory219856000
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
systime0.123981
time0.266020059586
usrtime0.051992
working_directory/project2/NextGenMapTest/Teaser/tests_generated/D2_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
memory238432000
return0
status1
stderr

None
stdout

239543 reads; of these:

  239543 (100.00%) were unpaired; of these:

    17347 (7.24%) aligned 0 times

    188600 (78.73%) aligned exactly 1 time

    33596 (14.03%) aligned >1 times

92.76% overall alignment rate
systime0.508922
time13.850894928
usrtime49.719441
working_directory/project2/NextGenMapTest/Teaser/tests_generated/D2_n