Skip to main content

Table 1 Summary of individual sequencing runs

From: Long-read individual-molecule sequencing reveals CRISPR-induced genetic heterogeneity in human ESCs

Gene

Mutant allele frequency (%) / Type

Amplicon size

Sequencing platform

Read count

Reads with UMI

UMI groups for variant calling

(≥ 5 reads)

Median read number per UMI group

UMI groups with introduced mutation

Somatic SNV count

Somatic SNV load per megabase

SV groups

EPOR

1:100 (1%)

168 bp

Nanopore

17,634

6444

284

7

2 (0.7%)

0

N/A

N/A

EPOR

1:1000 (0.1%)

6789 bp

PacBio

227,206

136,399

3184

6

4 (0.126%)

192

9.0

3

EPOR

1:10,000 (0.01%)

168 bp

Nanopore

1,093,683

494,009

15,598

8

1 (0.006%)

10

7.1

N/A

EPOR

1:10,000 (0.01%)

168 bp

Illumina

7,488,257

7,236,007

132,341

7

5 (0.004%)

85

7.1

N/A

PANX1 (Pan1)

WT

7077 bp

Nanopore

576,583

165,628

2810

6

N/A

73

3.8

0

PANX1 (Pan3)

WT

6595 bp

Nanopore

389,726

133,215

3867

7

N/A

103

4.1

0

PANX1 (Pan1)

Cas9 editing

7077 bp

Nanopore

2,761,805

613,147

3479

7

N/A

275

11.3

189 (5.4%)

PANX1 (Pan3)

Cas9 editing

6595 bp

Nanopore

3,078,165

1,042,582

7281

10

N/A

624

13.1

204 (2.8%)