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Edit and run 





In [12]:



    


config = {
    'data_folder'   : 'probes',
    'RUN'           : 'run_BWA_JKL_23_JU_1_orig',
    'chromosome'    : 'SL2.40ch12',
    'scaffold'      : 'SL2.40sc04878',
    'out_folder'    : 'reports_short'
}

if True:
    config['BAC'            ] = 'JBSC0201'
    config['BAC_coord_start'] = 622710
    config['BAC_coord_end'  ] = 624594
    config['BAC_coord'      ] = '%012d-%012d' % ( config['BAC_coord_start'], config['BAC_coord_end'  ] )
    config['RUN'            ] = 'run_BWA_JKL_23_JU_1_orig_PROBES'



    











In [13]:



    


%run -i probes_cfg_short.ipynb



    











In [14]:



    


%run -i probes_cfg_short_header.ipynb



    


















    







Singularity Report










    







Run:             run_BWA_JKL_23_JU_1_orig_PROBES










    







Chromosome:      SL2.40ch12










    







Scaffold:        SL2.40sc04878










    







BAC:             JBSC0201










    







BAC coord start: 622710










    







BAC coord end:   624594










    






Config
	BAC            : JBSC0201
	BAC_coord      : 000000622710-000000624594
	BAC_coord_end  : 624594
	BAC_coord_start: 622710
	RUN            : run_BWA_JKL_23_JU_1_orig_PROBES
	chromosome     : SL2.40ch12
	data_folder    : probes
	out_extensions : ['eps', 'png', 'pdf']
	out_folder     : reports_short
	scaffold       : SL2.40sc04878
Max Rows     : 10000
Column Names
	K-mer Coverage averaged: 50 Kbp
	Sequencing Coverage
	BLAST Coverage
	Ns
	AGP Contig
	AGP Gap

















In [16]:



    


%run -i probes_cfg_short_images.ipynb



    


















    






has config global
Populating the interactive namespace from numpy and matplotlib










    






WARNING: pylab import has clobbered these variables: ['axes', 'f', 'axis', 'title']
`%matplotlib` prevents importing * from pylab and numpy










    







Files










    







Input Files










    






KmerCoverageFile      : True  probes/run_BWA_JKL_23_JU_1_orig_PROBES/S_lycopersicum_chromosomes.fa_S_lycopersicum_scaffolds.sam.SL2.40ch12.SL2.40sc04878.JBSC0201_primer.000000622710-000000624594.S_lycopersicum_chromosomes.fa_S_lycopersicum_scaffolds.sam.SL2.40ch12.sam.SL2.40sc04878.sam.cov.prop.cov.gz
SequencingCoverageFile: True  probes/run_BWA_JKL_23_JU_1_orig_PROBES/S_lycopersicum_chromosomes.fa_S_lycopersicum_scaffolds.sam.SL2.40ch12.SL2.40sc04878.JBSC0201_primer.000000622710-000000624594.S_lycopersicum_chromosomes.fa_S_lycopersicum_chromosomes.pos.SL2.40ch12.pos.cov.SL2.40sc04878.cov.gz
AgpContigFile         : True  probes/run_BWA_JKL_23_JU_1_orig_PROBES/S_lycopersicum_chromosomes.fa_S_lycopersicum_scaffolds.sam.SL2.40ch12.SL2.40sc04878.JBSC0201_primer.000000622710-000000624594.S_lycopersicum_scaffolds_from_contigs.2.40.agp.SL2.40sc04878.agp.contig.agp.cov.gz
AgpGapFile            : True  probes/run_BWA_JKL_23_JU_1_orig_PROBES/S_lycopersicum_chromosomes.fa_S_lycopersicum_scaffolds.sam.SL2.40ch12.SL2.40sc04878.JBSC0201_primer.000000622710-000000624594.S_lycopersicum_scaffolds_from_contigs.2.40.agp.SL2.40sc04878.agp.gap.agp.cov.gz
AgpOtherFile          : True  probes/run_BWA_JKL_23_JU_1_orig_PROBES/S_lycopersicum_chromosomes.fa_S_lycopersicum_scaffolds.sam.SL2.40ch12.SL2.40sc04878.JBSC0201_primer.000000622710-000000624594.S_lycopersicum_scaffolds_from_contigs.2.40.agp.SL2.40sc04878.agp.other.agp.cov.gz
AgpUnknownFile        : True  probes/run_BWA_JKL_23_JU_1_orig_PROBES/S_lycopersicum_chromosomes.fa_S_lycopersicum_scaffolds.sam.SL2.40ch12.SL2.40sc04878.JBSC0201_primer.000000622710-000000624594.S_lycopersicum_scaffolds_from_contigs.2.40.agp.SL2.40sc04878.agp.unknown.agp.cov.gz
NsFile                : True  probes/run_BWA_JKL_23_JU_1_orig_PROBES/S_lycopersicum_chromosomes.fa_S_lycopersicum_scaffolds.sam.SL2.40ch12.SL2.40sc04878.JBSC0201_primer.000000622710-000000624594.S_lycopersicum_scaffolds.fa_NONE.tab.SL2.40ch12.tab.SL2.40sc04878.tab.cov.gz
BlastCoverageFile     : True  probes/run_BWA_JKL_23_JU_1_orig_PROBES/S_lycopersicum_chromosomes.fa_S_lycopersicum_scaffolds.sam.SL2.40ch12.SL2.40sc04878.JBSC0201_primer.000000622710-000000624594_Product.fasta.blast.cov.gz

all files present










    







Output Files










    






BLAST Coverage Distribution     :
 - reports_short/eps/run_BWA_JKL_23_JU_1_orig_PROBES_SL2.40ch12_SL2.40sc04878_JBSC0201_000000622710-000000624594.BLAST_Coverage_Distribution.eps
 - reports_short/png/run_BWA_JKL_23_JU_1_orig_PROBES_SL2.40ch12_SL2.40sc04878_JBSC0201_000000622710-000000624594.BLAST_Coverage_Distribution.png
 - reports_short/pdf/run_BWA_JKL_23_JU_1_orig_PROBES_SL2.40ch12_SL2.40sc04878_JBSC0201_000000622710-000000624594.BLAST_Coverage_Distribution.pdf
BLAST Coverage Stats            :
 - reports_short/eps/run_BWA_JKL_23_JU_1_orig_PROBES_SL2.40ch12_SL2.40sc04878_JBSC0201_000000622710-000000624594.BLAST_Coverage_Stats.eps
 - reports_short/png/run_BWA_JKL_23_JU_1_orig_PROBES_SL2.40ch12_SL2.40sc04878_JBSC0201_000000622710-000000624594.BLAST_Coverage_Stats.png
 - reports_short/pdf/run_BWA_JKL_23_JU_1_orig_PROBES_SL2.40ch12_SL2.40sc04878_JBSC0201_000000622710-000000624594.BLAST_Coverage_Stats.pdf
Combined graph                  :
 - reports_short/eps/run_BWA_JKL_23_JU_1_orig_PROBES_SL2.40ch12_SL2.40sc04878_JBSC0201_000000622710-000000624594.Combined_graph.eps
 - reports_short/png/run_BWA_JKL_23_JU_1_orig_PROBES_SL2.40ch12_SL2.40sc04878_JBSC0201_000000622710-000000624594.Combined_graph.png
 - reports_short/pdf/run_BWA_JKL_23_JU_1_orig_PROBES_SL2.40ch12_SL2.40sc04878_JBSC0201_000000622710-000000624594.Combined_graph.pdf
Gaps Distribution               :
 - reports_short/eps/run_BWA_JKL_23_JU_1_orig_PROBES_SL2.40ch12_SL2.40sc04878_JBSC0201_000000622710-000000624594.Gaps_Distribution.eps
 - reports_short/png/run_BWA_JKL_23_JU_1_orig_PROBES_SL2.40ch12_SL2.40sc04878_JBSC0201_000000622710-000000624594.Gaps_Distribution.png
 - reports_short/pdf/run_BWA_JKL_23_JU_1_orig_PROBES_SL2.40ch12_SL2.40sc04878_JBSC0201_000000622710-000000624594.Gaps_Distribution.pdf
K-mer Coverage Distribution     :
 - reports_short/eps/run_BWA_JKL_23_JU_1_orig_PROBES_SL2.40ch12_SL2.40sc04878_JBSC0201_000000622710-000000624594.K-mer_Coverage_Distribution.eps
 - reports_short/png/run_BWA_JKL_23_JU_1_orig_PROBES_SL2.40ch12_SL2.40sc04878_JBSC0201_000000622710-000000624594.K-mer_Coverage_Distribution.png
 - reports_short/pdf/run_BWA_JKL_23_JU_1_orig_PROBES_SL2.40ch12_SL2.40sc04878_JBSC0201_000000622710-000000624594.K-mer_Coverage_Distribution.pdf
K-mer Coverage Stats            :
 - reports_short/eps/run_BWA_JKL_23_JU_1_orig_PROBES_SL2.40ch12_SL2.40sc04878_JBSC0201_000000622710-000000624594.K-mer_Coverage_Stats.eps
 - reports_short/png/run_BWA_JKL_23_JU_1_orig_PROBES_SL2.40ch12_SL2.40sc04878_JBSC0201_000000622710-000000624594.K-mer_Coverage_Stats.png
 - reports_short/pdf/run_BWA_JKL_23_JU_1_orig_PROBES_SL2.40ch12_SL2.40sc04878_JBSC0201_000000622710-000000624594.K-mer_Coverage_Stats.pdf
Ns Distribution                 :
 - reports_short/eps/run_BWA_JKL_23_JU_1_orig_PROBES_SL2.40ch12_SL2.40sc04878_JBSC0201_000000622710-000000624594.Ns_Distribution.eps
 - reports_short/png/run_BWA_JKL_23_JU_1_orig_PROBES_SL2.40ch12_SL2.40sc04878_JBSC0201_000000622710-000000624594.Ns_Distribution.png
 - reports_short/pdf/run_BWA_JKL_23_JU_1_orig_PROBES_SL2.40ch12_SL2.40sc04878_JBSC0201_000000622710-000000624594.Ns_Distribution.pdf
Sequencing Coverage Distribution:
 - reports_short/eps/run_BWA_JKL_23_JU_1_orig_PROBES_SL2.40ch12_SL2.40sc04878_JBSC0201_000000622710-000000624594.Sequencing_Coverage_Distribution.eps
 - reports_short/png/run_BWA_JKL_23_JU_1_orig_PROBES_SL2.40ch12_SL2.40sc04878_JBSC0201_000000622710-000000624594.Sequencing_Coverage_Distribution.png
 - reports_short/pdf/run_BWA_JKL_23_JU_1_orig_PROBES_SL2.40ch12_SL2.40sc04878_JBSC0201_000000622710-000000624594.Sequencing_Coverage_Distribution.pdf
Sequencing Coverage Stats       :
 - reports_short/eps/run_BWA_JKL_23_JU_1_orig_PROBES_SL2.40ch12_SL2.40sc04878_JBSC0201_000000622710-000000624594.Sequencing_Coverage_Stats.eps
 - reports_short/png/run_BWA_JKL_23_JU_1_orig_PROBES_SL2.40ch12_SL2.40sc04878_JBSC0201_000000622710-000000624594.Sequencing_Coverage_Stats.png
 - reports_short/pdf/run_BWA_JKL_23_JU_1_orig_PROBES_SL2.40ch12_SL2.40sc04878_JBSC0201_000000622710-000000624594.Sequencing_Coverage_Stats.pdf
all_data                        :
 - reports_short/eps/run_BWA_JKL_23_JU_1_orig_PROBES_SL2.40ch12_SL2.40sc04878_JBSC0201_000000622710-000000624594.raw_data.csv
 - reports_short/png/run_BWA_JKL_23_JU_1_orig_PROBES_SL2.40ch12_SL2.40sc04878_JBSC0201_000000622710-000000624594.raw_data.csv
 - reports_short/pdf/run_BWA_JKL_23_JU_1_orig_PROBES_SL2.40ch12_SL2.40sc04878_JBSC0201_000000622710-000000624594.raw_data.csv
all_data_full                   :
 - reports_short/eps/run_BWA_JKL_23_JU_1_orig_PROBES_SL2.40ch12_SL2.40sc04878_JBSC0201_000000622710-000000624594.K-raw_data.full.csv
 - reports_short/png/run_BWA_JKL_23_JU_1_orig_PROBES_SL2.40ch12_SL2.40sc04878_JBSC0201_000000622710-000000624594.K-raw_data.full.csv
 - reports_short/pdf/run_BWA_JKL_23_JU_1_orig_PROBES_SL2.40ch12_SL2.40sc04878_JBSC0201_000000622710-000000624594.K-raw_data.full.csv










    







Read Files










    







K-mer Coverage File










    






probes/run_BWA_JKL_23_JU_1_orig_PROBES/S_lycopersicum_chromosomes.fa_S_lycopersicum_scaffolds.sam.SL2.40ch12.SL2.40sc04878.JBSC0201_primer.000000622710-000000624594.S_lycopersicum_chromosomes.fa_S_lycopersicum_scaffolds.sam.SL2.40ch12.sam.SL2.40sc04878.sam.cov.prop.cov.gz
Loaded 1885 rows and 9 columns










    







Sequencing Coverage File










    






probes/run_BWA_JKL_23_JU_1_orig_PROBES/S_lycopersicum_chromosomes.fa_S_lycopersicum_scaffolds.sam.SL2.40ch12.SL2.40sc04878.JBSC0201_primer.000000622710-000000624594.S_lycopersicum_chromosomes.fa_S_lycopersicum_chromosomes.pos.SL2.40ch12.pos.cov.SL2.40sc04878.cov.gz
Loaded 1885 rows and 2 columns










    







BLAST










    






probes/run_BWA_JKL_23_JU_1_orig_PROBES/S_lycopersicum_chromosomes.fa_S_lycopersicum_scaffolds.sam.SL2.40ch12.SL2.40sc04878.JBSC0201_primer.000000622710-000000624594_Product.fasta.blast.cov.gz
Loaded 1885 rows and 2 columns










    







AGP










    







Contig










    






probes/run_BWA_JKL_23_JU_1_orig_PROBES/S_lycopersicum_chromosomes.fa_S_lycopersicum_scaffolds.sam.SL2.40ch12.SL2.40sc04878.JBSC0201_primer.000000622710-000000624594.S_lycopersicum_scaffolds_from_contigs.2.40.agp.SL2.40sc04878.agp.contig.agp.cov.gz
Loaded 1885 rows and 2 columns










    







Gap










    






probes/run_BWA_JKL_23_JU_1_orig_PROBES/S_lycopersicum_chromosomes.fa_S_lycopersicum_scaffolds.sam.SL2.40ch12.SL2.40sc04878.JBSC0201_primer.000000622710-000000624594.S_lycopersicum_scaffolds_from_contigs.2.40.agp.SL2.40sc04878.agp.gap.agp.cov.gz
Loaded 1885 rows and 2 columns










    







Unknown










    






probes/run_BWA_JKL_23_JU_1_orig_PROBES/S_lycopersicum_chromosomes.fa_S_lycopersicum_scaffolds.sam.SL2.40ch12.SL2.40sc04878.JBSC0201_primer.000000622710-000000624594.S_lycopersicum_scaffolds_from_contigs.2.40.agp.SL2.40sc04878.agp.unknown.agp.cov.gz
Loaded 1885 rows and 2 columns










    







Other










    






probes/run_BWA_JKL_23_JU_1_orig_PROBES/S_lycopersicum_chromosomes.fa_S_lycopersicum_scaffolds.sam.SL2.40ch12.SL2.40sc04878.JBSC0201_primer.000000622710-000000624594.S_lycopersicum_scaffolds_from_contigs.2.40.agp.SL2.40sc04878.agp.other.agp.cov.gz
Loaded 1885 rows and 2 columns










    







Ns










    






probes/run_BWA_JKL_23_JU_1_orig_PROBES/S_lycopersicum_chromosomes.fa_S_lycopersicum_scaffolds.sam.SL2.40ch12.SL2.40sc04878.JBSC0201_primer.000000622710-000000624594.S_lycopersicum_scaffolds.fa_NONE.tab.SL2.40ch12.tab.SL2.40sc04878.tab.cov.gz
Loaded 1885 rows and 2 columns










    







Merge










    






Saved 1885 rows and 16 columns










    







Stats










    







Describe










    






          Position  K-mer Coverage  K-mer Coverage averaged: 500 bp  \
count  1885.000000     1885.000000                      1885.000000   
mean    942.000000        0.928912                         0.927319   
std     544.296947        0.156683                         0.025626   
min       0.000000        0.000000                         0.866267   
25%     471.000000        0.956522                         0.916254   
50%     942.000000        1.000000                         0.938124   
75%    1413.000000        1.000000                         0.944112   
max    1884.000000        1.000000                         0.970060   

       K-mer Coverage averaged: 2.5 Kbp  K-mer Coverage averaged: 5 Kbp  \
count                       1885.000000                     1885.000000   
mean                           0.877353                        0.824340   
std                            0.043045                        0.035340   
min                            0.747405                        0.768638   
25%                            0.865967                        0.794841   
50%                            0.894042                        0.820653   
75%                            0.898823                        0.852308   
max                            0.933035                        0.894508   

       K-mer Coverage averaged: 50 Kbp  K-mer Coverage averaged: 1 Mbp  \
count                      1885.000000                     1885.000000   
mean                          0.551125                        0.392724   
std                           0.002655                        0.000017   
min                           0.545561                        0.392664   
25%                           0.548489                        0.392707   
50%                           0.551954                        0.392730   
75%                           0.553236                        0.392734   
max                           0.555662                        0.392750   

       K-mer Coverage averaged: 5 Kbp before  \
count                            1885.000000   
mean                                0.877517   
std                                 0.021404   
min                                 0.846379   
25%                                 0.858785   
50%                                 0.873260   
75%                                 0.903393   
max                                 0.914539   

       K-mer Coverage averaged: 5 Kbp after  AGP Contig  AGP Gap  AGP Unknown  \
count                           1885.000000        1885     1885         1885   
mean                               0.681991           1        0            0   
std                                0.032334           0        0            0   
min                                0.636786           1        0            0   
25%                                0.650774           1        0            0   
50%                                0.679464           1        0            0   
75%                                0.718143           1        0            0   
max                                0.731445           1        0            0   

       AGP Other    Ns  Sequencing Coverage  BLAST Coverage  
count       1885  1885          1885.000000     1885.000000  
mean           0     0           131.670027        1.770557  
std            0     0            24.259355        1.469075  
min            0     0            66.000000       -7.000000  
25%            0     0           121.000000        1.000000  
50%            0     0           134.000000        2.000000  
75%            0     0           148.000000        2.000000  
max            0     0           200.000000        9.000000  










    







Quantiles










    






0.010    0.173913
0.025    0.434783
0.050    0.608696
0.100    0.739130
0.200    0.913043
0.300    0.956522
0.400    1.000000
0.500    1.000000
0.600    1.000000
0.700    1.000000
0.800    1.000000
0.900    1.000000
0.950    1.000000
0.975    1.000000
0.990    1.000000
dtype: float64










    







Percentiles










    






count      1885
count == 1 1159
prop  == 1 0.614854111406










    







Median










    






Position                                 942.000000
K-mer Coverage                             1.000000
K-mer Coverage averaged: 500 bp            0.938124
K-mer Coverage averaged: 2.5 Kbp           0.894042
K-mer Coverage averaged: 5 Kbp             0.820653
K-mer Coverage averaged: 50 Kbp            0.551954
K-mer Coverage averaged: 1 Mbp             0.392730
K-mer Coverage averaged: 5 Kbp before      0.873260
K-mer Coverage averaged: 5 Kbp after       0.679464
AGP Contig                                 1.000000
AGP Gap                                    0.000000
AGP Unknown                                0.000000
AGP Other                                  0.000000
Ns                                         0.000000
Sequencing Coverage                      134.000000
BLAST Coverage                             2.000000
dtype: float64










    







MAD










    






Position                                 471.249867
K-mer Coverage                             0.096644
K-mer Coverage averaged: 500 bp            0.020402
K-mer Coverage averaged: 2.5 Kbp           0.033280
K-mer Coverage averaged: 5 Kbp             0.029042
K-mer Coverage averaged: 50 Kbp            0.002375
K-mer Coverage averaged: 1 Mbp             0.000014
K-mer Coverage averaged: 5 Kbp before      0.018596
K-mer Coverage averaged: 5 Kbp after       0.029301
AGP Contig                                 0.000000
AGP Gap                                    0.000000
AGP Unknown                                0.000000
AGP Other                                  0.000000
Ns                                         0.000000
Sequencing Coverage                       18.134685
BLAST Coverage                             0.949328
dtype: float64










    







Plot










    







K-mer Coverage Stats










    






Saving Image: reports_short/eps/run_BWA_JKL_23_JU_1_orig_PROBES_SL2.40ch12_SL2.40sc04878_JBSC0201_000000622710-000000624594.K-mer_Coverage_Stats.eps
Saving Image: reports_short/png/run_BWA_JKL_23_JU_1_orig_PROBES_SL2.40ch12_SL2.40sc04878_JBSC0201_000000622710-000000624594.K-mer_Coverage_Stats.png
Saving Image: reports_short/pdf/run_BWA_JKL_23_JU_1_orig_PROBES_SL2.40ch12_SL2.40sc04878_JBSC0201_000000622710-000000624594.K-mer_Coverage_Stats.pdf










    

















    







Sequencing Coverage Stats










    






Saving Image: reports_short/eps/run_BWA_JKL_23_JU_1_orig_PROBES_SL2.40ch12_SL2.40sc04878_JBSC0201_000000622710-000000624594.Sequencing_Coverage_Stats.eps
Saving Image: reports_short/png/run_BWA_JKL_23_JU_1_orig_PROBES_SL2.40ch12_SL2.40sc04878_JBSC0201_000000622710-000000624594.Sequencing_Coverage_Stats.png
Saving Image: reports_short/pdf/run_BWA_JKL_23_JU_1_orig_PROBES_SL2.40ch12_SL2.40sc04878_JBSC0201_000000622710-000000624594.Sequencing_Coverage_Stats.pdf










    

















    







BLAST Coverage Stats










    






Saving Image: reports_short/eps/run_BWA_JKL_23_JU_1_orig_PROBES_SL2.40ch12_SL2.40sc04878_JBSC0201_000000622710-000000624594.BLAST_Coverage_Stats.eps
Saving Image: reports_short/png/run_BWA_JKL_23_JU_1_orig_PROBES_SL2.40ch12_SL2.40sc04878_JBSC0201_000000622710-000000624594.BLAST_Coverage_Stats.png
Saving Image: reports_short/pdf/run_BWA_JKL_23_JU_1_orig_PROBES_SL2.40ch12_SL2.40sc04878_JBSC0201_000000622710-000000624594.BLAST_Coverage_Stats.pdf










    

















    







K-mer Coverage Distribution










    






Number of rows: 1873
Saving Image: reports_short/eps/run_BWA_JKL_23_JU_1_orig_PROBES_SL2.40ch12_SL2.40sc04878_JBSC0201_000000622710-000000624594.K-mer_Coverage_Distribution.eps
Saving Image: reports_short/png/run_BWA_JKL_23_JU_1_orig_PROBES_SL2.40ch12_SL2.40sc04878_JBSC0201_000000622710-000000624594.K-mer_Coverage_Distribution.png
Saving Image: reports_short/pdf/run_BWA_JKL_23_JU_1_orig_PROBES_SL2.40ch12_SL2.40sc04878_JBSC0201_000000622710-000000624594.K-mer_Coverage_Distribution.pdf










    

















    







Sequencing Coverage Distribution










    






Number of rows: 1885
Saving Image: reports_short/eps/run_BWA_JKL_23_JU_1_orig_PROBES_SL2.40ch12_SL2.40sc04878_JBSC0201_000000622710-000000624594.Sequencing_Coverage_Distribution.eps
Saving Image: reports_short/png/run_BWA_JKL_23_JU_1_orig_PROBES_SL2.40ch12_SL2.40sc04878_JBSC0201_000000622710-000000624594.Sequencing_Coverage_Distribution.png
Saving Image: reports_short/pdf/run_BWA_JKL_23_JU_1_orig_PROBES_SL2.40ch12_SL2.40sc04878_JBSC0201_000000622710-000000624594.Sequencing_Coverage_Distribution.pdf










    

















    







BLAST Coverage Distribution










    






Number of rows: 1754
Saving Image: reports_short/eps/run_BWA_JKL_23_JU_1_orig_PROBES_SL2.40ch12_SL2.40sc04878_JBSC0201_000000622710-000000624594.BLAST_Coverage_Distribution.eps
Saving Image: reports_short/png/run_BWA_JKL_23_JU_1_orig_PROBES_SL2.40ch12_SL2.40sc04878_JBSC0201_000000622710-000000624594.BLAST_Coverage_Distribution.png
Saving Image: reports_short/pdf/run_BWA_JKL_23_JU_1_orig_PROBES_SL2.40ch12_SL2.40sc04878_JBSC0201_000000622710-000000624594.BLAST_Coverage_Distribution.pdf










    

















    







Gaps Distribution










    






Number of rows: 0










    







Ns Distribution










    






Number of rows: 0










    







CSV Output










    






Original Size 1885 rows and 16 columns
no need to sample
Saving data to     : reports_short/eps/run_BWA_JKL_23_JU_1_orig_PROBES_SL2.40ch12_SL2.40sc04878_JBSC0201_000000622710-000000624594.raw_data.csv
Saving data to     : reports_short/png/run_BWA_JKL_23_JU_1_orig_PROBES_SL2.40ch12_SL2.40sc04878_JBSC0201_000000622710-000000624594.raw_data.csv
Saving data to     : reports_short/pdf/run_BWA_JKL_23_JU_1_orig_PROBES_SL2.40ch12_SL2.40sc04878_JBSC0201_000000622710-000000624594.raw_data.csv










    







Combined Graph










    






[['K-mer Coverage averaged: 50 Kbp', [0, 1], 4, {'color': 'orange'}], ['Sequencing Coverage', None, 10, {'color': 'green', 'kind': 'line', 'logy': True}], ['BLAST Coverage', [0, None], 5, {'color': 'blue'}], ['Ns', [0.1, 1], 0, {'color': 'grey'}], ['AGP Contig', [0.1, 1], 0, {'color': 'grey'}], ['AGP Gap', [0.1, 1], 0, {'color': 'grey'}], None, None, None, None, None, None, None, None, None]
Saving Image: reports_short/eps/run_BWA_JKL_23_JU_1_orig_PROBES_SL2.40ch12_SL2.40sc04878_JBSC0201_000000622710-000000624594.Combined_graph.eps
Saving Image: reports_short/png/run_BWA_JKL_23_JU_1_orig_PROBES_SL2.40ch12_SL2.40sc04878_JBSC0201_000000622710-000000624594.Combined_graph.png
Saving Image: reports_short/pdf/run_BWA_JKL_23_JU_1_orig_PROBES_SL2.40ch12_SL2.40sc04878_JBSC0201_000000622710-000000624594.Combined_graph.pdf

%run -i probes_cfg_short_footer.ipynb

Content source: sauloal/ipython

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