knock-knock is a tool for exploring, categorizing, and quantifying the full spectrum of sequence outcomes produced by CRISPR knock-in experiments.

This example output shows data from knock-in of sfGFP payload at the CLTA locus in HEK293T cells with a variety of HDR donor types, read out by Pacbio long-read sequencing.

How to use this table

How to interpret read diagrams

		Total relevant reads	WT	simple indel	complex indel	HDR	blunt misintegration	incomplete HDR	complex misintegration	concatenated misintegration	genomic insertion	uncategorized
demo	demo/unedited_1	10,239	97.24%	1.23%	0.54%				0.02%			0.98%
	demo/unedited_2	10,046	97.36%	1.12%	0.43%						0.01%	1.08%
	demo/unedited_3	10,503	97.46%	1.08%	0.41%				0.03%		0.01%	1.02%
	demo/no-donor_1	9,503	8.53%	81.10%	6.65%				0.53%		0.27%	2.91%
	demo/no-donor_2	10,012	8.56%	81.47%	6.14%			0.07%	0.57%		0.37%	2.82%
	demo/no-donor_3	10,762	8.24%	80.57%	6.98%			0.04%	0.71%		0.46%	3.00%
	demo/ssDNA_1	9,444		57.43%	5.59%	12.02%		15.62%	5.94%		0.58%	2.82%
	demo/ssDNA_2	10,176	0.04%	58.82%	6.68%	11.53%		14.78%	5.02%		0.51%	2.61%
	demo/ssDNA_3	9,367	0.01%	57.98%	5.67%	12.80%	0.03%	14.56%	5.94%		0.46%	2.55%
	demo/PCR-unmodified_1	8,200	0.22%	65.83%	5.83%	10.06%	5.84%	2.84%	4.94%	0.73%	0.46%	3.24%
	demo/PCR-unmodified_2	7,593	0.16%	67.07%	5.25%	10.15%	5.91%	2.66%	4.24%	0.79%	0.67%	3.08%
	demo/PCR-unmodified_3	8,934	0.24%	65.13%	4.79%	10.71%	6.03%	2.75%	5.40%	0.77%	0.67%	3.50%
	demo/PCR-biotin_1	8,709	0.28%	59.16%	4.04%	19.80%	4.90%	3.96%	5.35%	0.23%	0.25%	2.03%
	demo/PCR-biotin_2	6,899	0.46%	60.72%	3.16%	20.00%	4.07%	3.91%	4.80%	0.20%	0.49%	2.17%
	demo/PCR-biotin_3	9,590	0.08%	58.54%	3.52%	22.54%	4.18%	4.07%	4.62%	0.18%	0.33%	1.93%
	demo/PCR-hybrid_1	6,713	0.10%	65.08%	3.96%	14.27%	2.25%	5.24%	5.79%	0.40%	0.60%	2.29%
	demo/PCR-hybrid_2	8,064	0.66%	64.93%	4.40%	14.72%	2.33%	4.34%	5.63%	0.24%	0.35%	2.41%
	demo/PCR-hybrid_3	8,541	0.30%	60.88%	4.37%	18.89%	2.19%	4.64%	5.43%	0.64%	0.39%	2.27%