QC pipeline metrics

|Column|Description| |——|———–| |multiplier|during parameter searching, the set [1..6] that was chosen| |MSRSI_non_integerness|median of segment residuals from segment integer copy number states| |MBRSI_dispersion_non_integerness|median of bin residuals from segment integer copy number states| |MBRSM_dispersion|median of bin residuals from segment median copy number values| |autocorrelation_hmmcopy|hmmcopy copy autocorrelation| |cv_hmmcopy|| |empty_bins_hmmcopy|number of empty bins in hmmcopy| |mad_hmmcopy|median absolute deviation of hmmcopy copy| |mean_hmmcopy_reads_per_bin|mean reads per hmmcopy bin| |median_hmmcopy_reads_per_bin|median reads per hmmcopy bin| |std_hmmcopy_reads_per_bin|standard deviation value of reads in hmmcopy bins| |total_mapped_reads_hmmcopy|total mapped reads in all hmmcopy bins| |total_halfiness|summed halfiness penality score of the cell| |scaled_halfiness|summed scaled halfiness penalty score of the cell| |mean_state_mads|mean value for all median absolute deviation scores for each state| |mean_state_vars|variance value for all median absolute deviation scores for each state| |mad_neutral_state|median absolute deviation score of the neutral 2 copy state| |breakpoints|number of breakpoints, as indicated by state changes not at the ends of chromosomes| |mean_copy|mean hmmcopy copy value| |state_mode|the most commonly occuring state| |log_likelihood|hmmcopy log likelihood for the cell| |true_multiplier|the exact decimal value used to scale the copy number for segmentation| |cell_id|label of the cell| |order|order of the cell in the hierarchical clustering tree| |index_sequence|index sequence of the adaptor sequence| |column|column of the cell on the nanowell chip| |img_col|column of the cell from the perspective of the microscope| |index_i5|id of the i5 index adapter sequence| |sample_type|type of the sample| |primer_i7|id of the i5 index primer sequence| |experimental_condition|experimental treatment of the cell, includes controls| |index_i7|id of the i7 index adapter sequence| |cell_call|living/dead classification of the cell based on staining usually, C1 == living, C2 == dead| |sample_id|name of the sample| |primer_i5|id of the i5 index primer sequence| |row|row of the cell on the nanowell chip| |quality|random forest classifier proability score that cell is good| |estimated_library_size|scaled total number of mapped reads| |total_mapped_reads|total number of mapped reads| |nohit|number of reads with no organism match| |salmon_multihit|number of reads that were classified as salmon and something else| |total_duplicate_reads|number of duplicate reads| |percent_duplicate_reads|percentage of duplicate reads| |total_properly_paired|number of properly paired reads| |mean_insert_size|mean insert size between paired reads| |coverage_breadth|percentage of genome covered by some read| |grch37|number of reads that were classified as human| |unpaired_duplicate_reads|number of unpaired duplicated reads| |unpaired_mapped_reads|number of unpaired mapped reads| |unmapped_reads|number of unmapped reads| |coverage_depth|average reads per nucleotide position in the genome| |median_insert_size|median insert size between paired reads| |salmon|number of reads that were classified as salmon| |grch37_multihit|number of reads that were classified as human and something else| |mm10|number of reads that were classified as mouse| |total_reads|total number of reads, regardless of mapping status| |standard_deviation_insert_size|standard deviation of the insert size between paired reads| |paired_mapped_reads|number of mapped reads that were properly paired| |mm10_multihit|number of reads classified as mouse and something else| |paired_duplicate_reads|number of paired reads that were also marked as duplicate| |is_contaminated|boolean, set to True if most reads belong to a different genome|