DOI: 10.5281/zenodo.5725622
title: Clonal decomposition and DNA replication states defined by scaled single cell genome sequencing

description: <strong>OV2295 Tables</strong> ov2295_breakpoint_counts.csv.gz: Table of breakpoint counts per cell prediction_id: identifier for the breakpoint cell_id: identifier for the cell read_count: number of reads library_id: identifier for the DNA library sample_id: identifier for the sequenced sample chromosome_1: chromosome of breakend 1 strand_1: orientation of break end 1 position_1: position of break end 1 chromosome_2: chromosome of breakend 2 strand_2: orientation of break end 2 position_2: position of break end 2 ov2295_cell_cn.csv.gz: Table of cell specific copy number cell_id: identifier for the cell sample_id: identifier for the sequenced sample library_id: identifier for the DNA library chr: chromosome of bin start: start of bin end: end of bin reads: number of reads copy: raw normalized copy number state: copy number state gc: percent gc of the bin map: average mappability of the bin ov2295_cell_metrics.csv.gz: Table of cell metrics cell_id: identifier of the cell unpaired_mapped_reads: number of unpaired mapped reads paired_mapped_reads: number of mapped reads that were properly paired unpaired_duplicate_reads: number of unpaired duplicated reads paired_duplicate_reads: number of paired reads that were also marked as duplicate unmapped_reads: number of unmapped reads percent_duplicate_reads: percentage of duplicate reads estimated_library_size: scaled total number of mapped reads total_reads: total number of reads, regardless of mapping status total_mapped_reads: total number of mapped reads total_duplicate_reads: number of duplicate reads total_properly_paired: number of properly paired reads coverage_breadth: percentage of genome covered by some read coverage_depth: average reads per nucleotide position in the genome median_insert_size: median insert size between paired reads mean_insert_size: mean insert size between paired reads standard_deviation_insert_size: standard deviation of the insert size between paired reads 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 library_id: identifier for the DNA library index: ignored 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: ignored 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_halfiness: summed halfiness penality score of the cell total_mapped_reads_hmmcopy: total mapped reads in all hmmcopy bins 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 order: order of the cell in the hierarchical clustering tree quality: random forest classifier proability score that cell is good ov2295_clone_alleles.csv.gz: Table of clone specific allele data chr: chromosome of bin start: start of bin end: end of bin hap_label: haplotype block identifier clone_id: clone identifier allele_1_sum: number of reads for allele 1 of the haplotype block allele_2_sum: number of reads for allele 2 of the haplotype block total_counts_sum: total reads for the haplotype block ov2295_clone_breakpoints.csv.gz: Table of breakpoints per clone for OV2295 samples. Columns: prediction_id: identifier for the breakpoint chromosome_1: chromosome of breakend 1 strand_1: orientation of break end 1 position_1: position of break end 1 chromosome_2: chromosome of breakend 2 strand_2: orientation of break end 2 position_2: position of break end 2 clone_id: clone identifier read_count: number of reads is_present: presence=1, absent=0 ov2295_clone_clusters.csv.gz: Table of cell clusters as putative clones cell_id: identifier for the cell clone_id: clone identifier ov2295_clone_cn.csv.gz: Table of allele specific copy number per clone for OV2295 samples. Columns: chr: chromosome of bin start: start of bin end: end of bin total_cn: HMMCopy predicted total copy number minor_cn: HMM predicted minor copy number major_cn: HMM predicted major copy number clone_id: clone identifier ov2295_clone_snvs.csv.gz: Table of SNVs per clone for OV2295 samples. Columns: chrom: chromosome coord: genome position ref: reference nucleotide alt: alternate nucleotide clone_id: clone identifier ref_counts: number of reads at this position matching the reference nucleotide alt_counts: number of reads at this position matching the alternate nucleotide total_counts: total number of reads at this position is_present: presence=0, absent=1 is_het: is heterozygous is_hom: is homozygous for the alternate ov2295_nodes.csv.gz: Table of phylogenetic information for SNV evolution variant_id: identifier for the SNV as chrom:coord:ref:alt node: node in the phylogenetic tree loss: probability the SNV was lost at this node origin: probability the SNV originated at this node presence: probability the SNV is present at this node ml_origin: binary indicator the SNV originated at this node ml_presence: binary indicator the SNV is present at this node ml_loss: binary indicator the SNV was lost at this node ov2295_snv_counts.csv.gz: Table of SNV counts chrom: chromosome coord: genome position ref: reference nucleotide alt: alternate nucleotide ref_counts: number of reads at this position matching the reference nucleotide alt_counts: number of reads at this position matching the alternate nucleotide cell_id: identifier for the cell total_counts: total number of reads at this position sample_id: identifier for the sequenced sample ov2295_tree.pickle: Phylogenetic tree in python pickle format. Requires installation of the stochastic dollo code at: https://bitbucket.org/dranew/dollo, version 0.4.2. Note the following sample mapping: ‘SA922’: ‘OV2295(R2)’, ‘SA921’: ‘TOV2295(R)’, ‘SA1090’: ‘OV2295’, <strong>Plots</strong> ov_supp_clone_allele_cn.png: Clone allele ratios for each OV2295 sample. ov_supp_clone_total_cn.png: Clone copy number for each OV2295 sample. ov_supp_sample_total_cn.png: Bulk copy number for each OV2295 sample. ov_supp_sample_allele_cn.png: Bulk allele ratios for each OV2295 sample.