var_names	labels
experiment	ID of C1 chip (i.e. processing date in YYYYMMDD)
well	Well of C1 chip (96 total, rows A-H, cols 1-12)
cell_number	The number of cells observed in the well via microscopy
concentration	The cDNA concentration of the well prior to library prep
ERCC	The dilution factor of the ERCC spike-ins
individual.1	Individual # 1 included on this C1 chip
individual.2	Individual # 2 included on this C1 chip
image_individual	The chip label for the image files
image_label	The well label for the image files
raw	The number of raw reads
umi	The number of reads with a valid UMI
mapped	The number of reads with a valid UMI that mapped to a genome
unmapped	The number of reads with a valid UMI that did *not* map to a genome
reads_ercc	The number of reads that mapped to the ERCC spike-in transcripts
reads_hs	The number of reads that mapped to the H. sapiens genome
reads_egfp	The number of reads that mapped to the FUCCI EGFP transgene
reads_mcherry	The number of reads that mapped to the FUCCI mCherry transgene
molecules	The number of molecules (i.e. post UMI-deduplication)
mol_ercc	The number of molecules that mapped to the ERCC spike-in transcripts
mol_hs	The number of molecules that mapped to the H. sapiens genome
mol_egfp	The number of molecules that mapped to the FUCCI EGFP transgene
mol_mcherry	The number of molecules that mapped to the FUCCI mCherry transgene
detect_ercc	The number of ERCC genes with at least one molecule
detect_hs	The number of H. sapiens genes with at least one molecule
chip_id	verifyBamID: The predicted individual based on the sequencing data
chipmix	verifyBamID: chipmix is a metric for detecting sample swaps
freemix	verifyBamID: freemix is a measure of contamination. 0 == good & 0.5 == bad
snps	verifyBamID: The number of SNPs that passed thresholds for AF and missingness
reads	verifyBamID: The number of sequences that overlapped SNPs
avg_dp	verifyBamID: The average sequencing depth that covered a SNP
min_dp	verifyBamID: A minimun depth threshold for QC only (affects snps_w_min)
snps_w_min	verifyBamID: The number of SNPs that had the minimum depth (min_dp); QC only
valid_id	verifyBamID: Is the predicted individual 1 of the 2 added to the C1 chip?
cut_off_reads	QC filter: number of mapped reads > 85th percentile among zero-cell samples
unmapped_ratios	QC filter: among reads with a valid UMI, number of unmapped/number of mapped (unmapped/umi)
cut_off_unmapped	QC filter: unmapped ratio < 30th percentile among zero-cell samples
ercc_percentage	QC filter: number of reads mapped to ERCC/total sample mapped reads (reads_ercc/mapped)
cut_off_ercc	QC filter: ercc percentage < 15th percentile among zero-cell samples
cut_off_genes	QC filter: number of endogenous genes with at least one molecule (detect_hs) > 85th percentile among zero-cell samples
ercc_conversion	QC filter: among ERCC, number of molecules/number of mapped reads (mol_ercc/reads_ercc)
conversion	QC filter: among endogenous genes, number of molecules/number of mapped reads (mol_hs/reads_hs)
conversion_outlier	QC filter: microscopy detects 1 cell AND ERCC conversion rate > .094
molecule_outlier	QC filter: Is the sample an outlier in total molecule count?
filter_all	QC filter: Does the sample pass all the QC filters? cell_number==1, mol_egfp >0, valid_id==1, cut_off_reads==TRUE, cut_off_ercc==TRUE, cut_off_genes=TRUE
rfp.median.log10sum	mCherry background-corrected intensity (log10sum)
gfp.median.log10sum	EGFP background-corrected intensity (log10sum)
dapi.median.log10sum	DAPI background-corrected intensity (log10sum)
rfp.median.log10sum.adjust	mCherry background-corrected intensity adjusted for C1 batch(log10sum)
gfp.median.log10sum.adjust	EGFP background-corrected intensity adjusted for C1 batch (log10sum)
dapi.median.log10sum.adjust	DAPI background-corrected intensity adjusted for C1 batch (log10sum)
size	nucleus size
perimeter	nucleus perimeter
eccentricity	nucleus eccentricity
theta	cell time