README
A readme file that explains the information in the data files, some portions of the computational workflow, and the directory structure for replication of the computational workflow.
illustration_tagging_computing
An scalar vector illustration file of the workflow made using Inkscape 0.92.
schema_of_files
A text file describing the directory structure of the workflow.
samples_replicate_numbers
A two-column csv file indicating the sample name and replicate number for the appropriate experiment type (PCR-based or gDNA-based template).
samples_metadata
A csv file containing information on sample name, sample type, input variant allele fraction, observed variant allele fraction, and other information on various data file locations within the directory structure. All headers are explained in the README file.
dir_structure.tar
A tar 1.26 compressed file of the directory structure of the computational workflow for ease of replication. The subdirectories are empty of files. The use of this file is explained in the README file.
dir_structure.gz.tar
gDNA_stds_error_pos
A csv file documenting the observed error at targeted position (position 10 of reference) for each gDNA sample investigated.
KRAS_WT_144144_nuc_counts
A csv file containing the nucleotide counts for each position of gDNA WT sample, replicate 1.
KRAS_WT_145145_nuc_counts
A csv file containing the nucleotide counts for each position of gDNA WT sample, replicate 2.
KRAS_10-5_144145_nuc_counts
A csv file containing the nucleotide counts for each position of gDNA 10^-5 sample, replicate 1.
KRAS_10-5_145146_nuc_counts
A csv file containing the nucleotide counts for each position of gDNA 10^-5 sample, replicate 2.
KRAS_10-4_144146_nuc_counts
A csv file containing the nucleotide counts for each position of gDNA 10^-4 sample, replicate 1.
KRAS_10-4_145147_nuc_counts
A csv file containing the nucleotide counts for each position of gDNA 10^-4 sample, replicate 2.
KRAS_10-3_144147_nuc_counts
A csv file containing the nucleotide counts for each position of gDNA 10^-3 sample, replicate 1.
KRAS_10-3_145148_nuc_counts
A csv file containing the nucleotide counts for each position of gDNA 10^-3 sample, replicate 2.
KRAS_10-2_144148_nuc_counts
A csv file containing the nucleotide counts for each position of gDNA 10^-2 sample, replicate 1.
KRAS_10-2_145149_nuc_counts
A csv file containing the nucleotide counts for each position of gDNA 10^-2 sample, replicate 2.
KRAS_10-1_144149_nuc_counts
A csv file containing the nucleotide counts for each position of gDNA 10^-1 sample, replicate 1.
KRAS_10-1_145150_nuc_counts
A csv file containing the nucleotide counts for each position of gDNA 10^-1 sample, replicate 2.
KRAS_MUT_144150_nuc_counts
A csv file containing the nucleotide counts for each position of gDNA mutant only sample, replicate 1.
KRAS_MUT_145151_nuc_counts
A csv file containing the nucleotide counts for each position of gDNA mutant only sample, replicate 2.
gDNA_all_group_size_histo
A csv file containing data describing the number of groups with specified number of reads in the group for the gDNA samples. The first column indicates the number of reads, the remaining column headers are the sample names, and the list of numbers under each name is the number of groups of specified read depth.
gDNA_all_group_read_lens_histo
A csv file of the read lengths for each gDNA sample, with length as the row name and the number of reads with specified length for each sample across the columns. Column headers are the names of the samples.
KRAS_WT_144144_read_quals
A csv documenting the median qualities of each position for each tag group in gDNA WT sample, replicate1. The header information is in the README.txt file.
KRAS_WT_145145_read_quals
A csv documenting the median qualities of each position for each tag group in gDNA WT sample, replicate2. The header information is in the README.txt file.
KRAS_10-5_144145_read_quals
A csv documenting the median qualities of each position for each tag group in gDNA 10^-5 sample, replicate1. The header information is in the README.txt file.
KRAS_10-5_145146_read_quals
A csv documenting the median qualities of each position for each tag group in gDNA 10^-5 sample, replicate2. The header information is in the README.txt file.
KRAS_10-4_144146_read_quals
A csv documenting the median qualities of each position for each tag group in gDNA 10^-4 sample, replicate1. The header information is in the README.txt file.
KRAS_10-4_145147_read_quals
A csv documenting the median qualities of each position for each tag group in gDNA 10^-4 sample, replicate2. The header information is in the README.txt file.
KRAS_10-3_144147_read_quals
A csv documenting the median qualities of each position for each tag group in gDNA 10^-3 sample, replicate1. The header information is in the README.txt file.
KRAS_10-3_145148_read_quals
A csv documenting the median qualities of each position for each tag group in gDNA 10^-3 sample, replicate2. The header information is in the README.txt file.
KRAS_10-2_144148_read_quals
A csv documenting the median qualities of each position for each tag group in gDNA 10^-2 sample, replicate1. The header information is in the README.txt file.
KRAS_10-2_145149_read_quals
A csv documenting the median qualities of each position for each tag group in gDNA 10^-2 sample, replicate2. The header information is in the README.txt file.
KRAS_10-1_144149_read_quals
A csv documenting the median qualities of each position for each tag group in gDNA 10^-1 sample, replicate1. The header information is in the README.txt file.
KRAS_10-1_145150_read_quals
A csv documenting the median qualities of each position for each tag group in gDNA 10^-1 sample, replicate2. The header information is in the README.txt file.
KRAS_MUT_144150_read_quals
A csv documenting the median qualities of each position for each tag group in gDNA mutant only sample, replicate1. The header information is in the README.txt file.
KRAS_MUT_145151_read_quals
A csv documenting the median qualities of each position for each tag group in gDNA mutant only sample, replicate2. The header information is in the README.txt file.
KRAS_WT_144144_filtered.csv
A gzipped csv documenting the tag, read sequence, and associated qualities of all reads matching the majority read length (documented in read lengths csv) of gDNA WT only sample, replicate1. The header information is in the README.txt file.
KRAS_WT_145145_filtered.csv
A gzipped csv documenting the tag, read sequence, and associated qualities of all reads matching the majority read length (documented in read lengths csv) of gDNA WT only sample, replicate2. The header information is in the README.txt file.
KRAS_10-5_144145_filtered.csv
A gzipped csv documenting the tag, read sequence, and associated qualities of all reads matching the majority read length (documented in read lengths csv) of gDNA 10^-5 sample, replicate1. The header information is in the README.txt file.
KRAS_10-5_145146_filtered.csv
A gzipped csv documenting the tag, read sequence, and associated qualities of all reads matching the majority read length (documented in read lengths csv) of gDNA 10^-5 sample, replicate2. The header information is in the README.txt file.
KRAS_10-4_144146_filtered.csv
A gzipped csv documenting the tag, read sequence, and associated qualities of all reads matching the majority read length (documented in read lengths csv) of gDNA 10^-4 sample, replicate1. The header information is in the README.txt file.
KRAS_10-4_145147_filtered.csv
A gzipped csv documenting the tag, read sequence, and associated qualities of all reads matching the majority read length (documented in read lengths csv) of gDNA 10^-4 sample, replicate2. The header information is in the README.txt file.
KRAS_10-3_144147_filtered.csv
A gzipped csv documenting the tag, read sequence, and associated qualities of all reads matching the majority read length (documented in read lengths csv) of gDNA 10^-3 sample, replicate1. The header information is in the README.txt file.
KRAS_10-3_145148_filtered.csv
A gzipped csv documenting the tag, read sequence, and associated qualities of all reads matching the majority read length (documented in read lengths csv) of gDNA 10^-3 sample, replicate2. The header information is in the README.txt file.
KRAS_10-2_144148_filtered.csv
A gzipped csv documenting the tag, read sequence, and associated qualities of all reads matching the majority read length (documented in read lengths csv) of gDNA 10^-2 sample, replicate1. The header information is in the README.txt file.
KRAS_10-2_145149_filtered.csv
A gzipped csv documenting the tag, read sequence, and associated qualities of all reads matching the majority read length (documented in read lengths csv) of gDNA 10^-2 sample, replicate2. The header information is in the README.txt file.
KRAS_10-1_144149_filtered.csv
A gzipped csv documenting the tag, read sequence, and associated qualities of all reads matching the majority read length (documented in read lengths csv) of gDNA 10^-1 sample, replicate1. The header information is in the README.txt file.
KRAS_10-1_145150_filtered.csv
A gzipped csv documenting the tag, read sequence, and associated qualities of all reads matching the majority read length (documented in read lengths csv) of gDNA 10^-1 sample, replicate2. The header information is in the README.txt file.
KRAS_MUT_144150_filtered.csv
A gzipped csv documenting the tag, read sequence, and associated qualities of all reads matching the majority read length (documented in read lengths csv) of gDNA mutant only sample, replicate1. The header information is in the README.txt file.
KRAS_MUT_145151_filtered.csv
A gzipped csv documenting the tag, read sequence, and associated qualities of all reads matching the majority read length (documented in read lengths csv) of gDNA mutant only sample, replicate2. The header information is in the README.txt file.
PCR_stds_error_pos
A csv file documenting the observed error at targeted position (position 10 of reference) for each PCR-based sample investigated.
Kras_WT_132132_nuc_counts
A csv file containing the nucleotide counts for each position of PCR-based WT sample, replicate 1.
Kras_WT_132133_nuc_counts
A csv file containing the nucleotide counts for each position of PCR-based WT sample, replicate 2.
Kras_WT_132134_nuc_counts
A csv file containing the nucleotide counts for each position of PCR-based WT sample, replicate 3.
Kras_10-5_132135_nuc_counts
A csv file containing the nucleotide counts for each position of PCR-based 10^-5 sample, replicate 1.
Kras_10-5_132136_nuc_counts
A csv file containing the nucleotide counts for each position of PCR-based 10^-5 sample, replicate 2.
Kras_10-5_132149_nuc_counts
A csv file containing the nucleotide counts for each position of PCR-based 10^-5 sample, replicate 3.
Kras_10-4_132137_nuc_counts
A csv file containing the nucleotide counts for each position of PCR-based 10^-4 sample, replicate 1.
Kras_10-4_132138_nuc_counts
A csv file containing the nucleotide counts for each position of PCR-based 10^-4 sample, replicate 2.
Kras_10-4_132139_nuc_counts
A csv file containing the nucleotide counts for each position of PCR-based 10^-4 sample, replicate 3.
Kras_10-3_132140_nuc_counts
A csv file containing the nucleotide counts for each position of PCR-based 10^-3 sample, replicate 1.
Kras_10-3_132141_nuc_counts
A csv file containing the nucleotide counts for each position of PCR-based 10^-3 sample, replicate 2.
Kras_10-3_132142_nuc_counts
A csv file containing the nucleotide counts for each position of PCR-based 10^-3 sample, replicate 3.
Kras_10-2_132143_nuc_counts
A csv file containing the nucleotide counts for each position of PCR-based 10^-2 sample, replicate 1.
Kras_10-2_132144_nuc_counts
A csv file containing the nucleotide counts for each position of PCR-based 10^-2 sample, replicate 2.
Kras_10-2_132145_nuc_counts
A csv file containing the nucleotide counts for each position of PCR-based 10^-2 sample, replicate 3.
Kras_10-1_132146_nuc_counts
A csv file containing the nucleotide counts for each position of PCR-based 10^-1 sample, replicate 1.
Kras_10-1_132147_nuc_counts
A csv file containing the nucleotide counts for each position of PCR-based 10^-1 sample, replicate 2.
Kras_10-1_132148_nuc_counts
A csv file containing the nucleotide counts for each position of PCR-based 10^-1 sample, replicate 3.
Kras_MUT_132150_nuc_counts
A csv file containing the nucleotide counts for each position of PCR-based mutant only sample, replicate 1.
Kras_MUT_132151_nuc_counts
A csv file containing the nucleotide counts for each position of PCR-based mutant only sample, replicate 2.
Kras_MUT_132152_nuc_counts
A csv file containing the nucleotide counts for each position of PCR-based mutant only sample, replicate 3.
PCR_all_group_size_histo
A csv file containing data describing the number of groups with specified number of reads in the group for the PCR-based samples. The first column indicates the number of reads, the remaining column headers are the sample names, and the list of numbers under each name is the number of groups of specified read depth.
PCR_all_group_read_lens_histo
A csv file of the read lengths for each PCR-based sample, with length as the row name and the number of reads with specified length for each sample across the columns. Column headers are the names of the samples.
Kras_WT_132132_read_quals
A csv documenting the median qualities of each position for each tag group in PCR-based WT sample, replicate1. The header information is in the README.txt file.
Kras_WT_132133_read_quals
A csv documenting the median qualities of each position for each tag group in PCR-based WT sample, replicate2. The header information is in the README.txt file.
Kras_WT_132134_read_quals
A csv documenting the median qualities of each position for each tag group in PCR-based WT sample, replicate3. The header information is in the README.txt file.
Kras_10-5_132135_read_quals
A csv documenting the median qualities of each position for each tag group in PCR-based 10^-5 sample, replicate1. The header information is in the README.txt file.
Kras_10-5_132136_read_quals
A csv documenting the median qualities of each position for each tag group in PCR-based 10^-5 sample, replicate2. The header information is in the README.txt file.
Kras_10-5_132149_read_quals
A csv documenting the median qualities of each position for each tag group in PCR-based 10^-5 sample, replicate3. The header information is in the README.txt file.
Kras_10-4_132137_read_quals
A csv documenting the median qualities of each position for each tag group in PCR-based 10^-4 sample, replicate1. The header information is in the README.txt file.
Kras_10-4_132138_read_quals
A csv documenting the median qualities of each position for each tag group in PCR-based 10^-4 sample, replicate2. The header information is in the README.txt file.
Kras_10-4_132139_read_quals
A csv documenting the median qualities of each position for each tag group in PCR-based 10^-4 sample, replicate3. The header information is in the README.txt file.
Kras_10-3_132140_read_quals
A csv documenting the median qualities of each position for each tag group in PCR-based 10^-3 sample, replicate1. The header information is in the README.txt file.
Kras_10-3_132141_read_quals
A csv documenting the median qualities of each position for each tag group in PCR-based 10^-3 sample, replicate2. The header information is in the README.txt file.
Kras_10-3_132142_read_quals
A csv documenting the median qualities of each position for each tag group in PCR-based 10^-3 sample, replicate3. The header information is in the README.txt file.
Kras_10-2_132143_read_quals
A csv documenting the median qualities of each position for each tag group in PCR-based 10^-2 sample, replicate1. The header information is in the README.txt file.
Kras_10-2_132144_read_quals
A csv documenting the median qualities of each position for each tag group in PCR-based 10^-2 sample, replicate2. The header information is in the README.txt file.
Kras_10-2_132145_read_quals
A csv documenting the median qualities of each position for each tag group in PCR-based 10^-2 sample, replicate3. The header information is in the README.txt file.
Kras_10-1_132146_read_quals
A csv documenting the median qualities of each position for each tag group in PCR-based 10^-1 sample, replicate1. The header information is in the README.txt file.
Kras_10-1_132147_read_quals
A csv documenting the median qualities of each position for each tag group in PCR-based 10^-1 sample, replicate2. The header information is in the README.txt file.
Kras_10-1_132148_read_quals
A csv documenting the median qualities of each position for each tag group in PCR-based 10^-1 sample, replicate3. The header information is in the README.txt file.
Kras_MUT_132150_read_quals
A csv documenting the median qualities of each position for each tag group in PCR-based mutant only sample, replicate1. The header information is in the README.txt file.
Kras_MUT_132151_read_quals
A csv documenting the median qualities of each position for each tag group in PCR-based mutant only sample, replicate2. The header information is in the README.txt file.
Kras_MUT_132152_read_quals
A csv documenting the median qualities of each position for each tag group in PCR-based mutant only sample, replicate3. The header information is in the README.txt file.
Kras_WT_132132_filtered.csv
A gzipped csv documenting the tag, read sequence, and associated qualities of all reads matching the majority read length (documented in read lengths csv) of PCR-based WT only sample, replicate1. The header information is in the README.txt file.
Kras_WT_132133_filtered.csv
A gzipped csv documenting the tag, read sequence, and associated qualities of all reads matching the majority read length (documented in read lengths csv) of PCR-based WT only sample, replicate2. The header information is in the README.txt file.
Kras_WT_132134_filtered.csv
A gzipped csv documenting the tag, read sequence, and associated qualities of all reads matching the majority read length (documented in read lengths csv) of PCR-based WT only sample, replicate3. The header information is in the README.txt file.
Kras_10-5_132135_filtered.csv
A gzipped csv documenting the tag, read sequence, and associated qualities of all reads matching the majority read length (documented in read lengths csv) of PCR-based 10^-5 only sample, replicate1. The header information is in the README.txt file.
Kras_10-5_132136_filtered.csv
A gzipped csv documenting the tag, read sequence, and associated qualities of all reads matching the majority read length (documented in read lengths csv) of PCR-based 10^-5 only sample, replicate2. The header information is in the README.txt file.
Kras_10-5_132149_filtered.csv
A gzipped csv documenting the tag, read sequence, and associated qualities of all reads matching the majority read length (documented in read lengths csv) of PCR-based 10^-5 only sample, replicate3. The header information is in the README.txt file.
Kras_10-4_132137_filtered.csv
A gzipped csv documenting the tag, read sequence, and associated qualities of all reads matching the majority read length (documented in read lengths csv) of PCR-based 10^-4 only sample, replicate1. The header information is in the README.txt file.
Kras_10-4_132138_filtered.csv
A gzipped csv documenting the tag, read sequence, and associated qualities of all reads matching the majority read length (documented in read lengths csv) of PCR-based 10^-4 only sample, replicate2. The header information is in the README.txt file.
Kras_10-4_132139_filtered.csv
A gzipped csv documenting the tag, read sequence, and associated qualities of all reads matching the majority read length (documented in read lengths csv) of PCR-based 10^-4 only sample, replicate3. The header information is in the README.txt file.
Kras_10-3_132140_filtered.csv
A gzipped csv documenting the tag, read sequence, and associated qualities of all reads matching the majority read length (documented in read lengths csv) of PCR-based 10^-3 only sample, replicate1. The header information is in the README.txt file.
Kras_10-3_132141_filtered.csv
A gzipped csv documenting the tag, read sequence, and associated qualities of all reads matching the majority read length (documented in read lengths csv) of PCR-based 10^-3 only sample, replicate2. The header information is in the README.txt file.
Kras_10-3_132142_filtered.csv
A gzipped csv documenting the tag, read sequence, and associated qualities of all reads matching the majority read length (documented in read lengths csv) of PCR-based 10^-3 only sample, replicate3. The header information is in the README.txt file.
Kras_10-2_132143_filtered.csv
A gzipped csv documenting the tag, read sequence, and associated qualities of all reads matching the majority read length (documented in read lengths csv) of PCR-based 10^-2 only sample, replicate1. The header information is in the README.txt file.
Kras_10-2_132144_filtered.csv
A gzipped csv documenting the tag, read sequence, and associated qualities of all reads matching the majority read length (documented in read lengths csv) of PCR-based 10^-2 only sample, replicate2. The header information is in the README.txt file.
Kras_10-2_132145_filtered.csv
A gzipped csv documenting the tag, read sequence, and associated qualities of all reads matching the majority read length (documented in read lengths csv) of PCR-based 10^-2 only sample, replicate3. The header information is in the README.txt file.
Kras_10-1_132146_filtered.csv
A gzipped csv documenting the tag, read sequence, and associated qualities of all reads matching the majority read length (documented in read lengths csv) of PCR-based 10^-1 only sample, replicate1. The header information is in the README.txt file.
Kras_10-1_132147_filtered.csv
A gzipped csv documenting the tag, read sequence, and associated qualities of all reads matching the majority read length (documented in read lengths csv) of PCR-based 10^-1 only sample, replicate2. The header information is in the README.txt file.
Kras_10-1_132148_filtered.csv
A gzipped csv documenting the tag, read sequence, and associated qualities of all reads matching the majority read length (documented in read lengths csv) of PCR-based 10^-1 only sample, replicate3. The header information is in the README.txt file.
Kras_MUT_132150_filtered.csv
A gzipped csv documenting the tag, read sequence, and associated qualities of all reads matching the majority read length (documented in read lengths csv) of PCR-based mutant only only sample, replicate1. The header information is in the README.txt file.
Kras_MUT_132151_filtered.csv
A gzipped csv documenting the tag, read sequence, and associated qualities of all reads matching the majority read length (documented in read lengths csv) of PCR-based mutant only only sample, replicate2. The header information is in the README.txt file.
Kras_MUT_132152_filtered.csv
A gzipped csv documenting the tag, read sequence, and associated qualities of all reads matching the majority read length (documented in read lengths csv) of PCR-based mutant only only sample, replicate3. The header information is in the README.txt file.