| cell_id |
label of the cell |
| 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 |
| 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 |