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 Mapped9607253.475%
Wrongly Mapped83074.624%
Not Mapped7527841.901%
Total179657100.0%
Read Failure Statistics
Not mapped7527841.901%
Missing in mapper output00.0%
Mapped to wrong chromosome45312.522%
Mapped to wrong position37762.102%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments0
F-Measure0.696900
Precision0.920400
Recall0.560700
Timing
Raw Mapping Time11.857s
Effective Mapping Time11.707s
Effective Init Time0.150s
Effective Time MeasureWall clock
Mapping Time (Wall)11.857s
Mapping Time (CPU)41.946s
Mapping Time (CPU User)41.239s
Mapping Time (CPU System)0.707s
Init Time (Wall)0.150s
Init Time (CPU)0.176s
Init Time (CPU User)0.064s
Init Time (CPU System)0.112s
Additional Information
Mapper Memory Usage242 MB
Total Test Runtime (Wall)22.774s
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
memory219832000
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
systime0.12898
time0.193641901016
usrtime0.056991
working_directory/project2/NextGenMapTest/Teaser/tests_generated/D3_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
systime0.111982
time0.150090932846
usrtime0.06399
working_directory/project2/NextGenMapTest/Teaser/tests_generated/D3_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
memory242952000
return0
status1
stderr

None
stdout

179657 reads; of these:

  179657 (100.00%) were unpaired; of these:

    75278 (41.90%) aligned 0 times

    90033 (50.11%) aligned exactly 1 time

    14346 (7.99%) aligned >1 times

58.10% overall alignment rate
systime0.706892
time11.8572690487
usrtime41.23873
working_directory/project2/NextGenMapTest/Teaser/tests_generated/D3_n