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Table 2 tSMS sequencing of ancient DNA extracts from sample TP (13,389 ± 52BP)

From: Improving the performance of true single molecule sequencing for ancient DNA

Sample

Platform

#

Conditions

#Seqs

nucDNA

bp

mtDNA

bp

%Endo.

TP1

110 V

1

80°C, Phosphatase

1,980,210

85,738

2,885,229

53

1,845

4.33%

 

110 V

1

80°C

234,094

28,797

998,007

8

255

12.30%

 

110 V

1

95°C

228,871

12,573

438,111

5

162

5.50%

TP1RE

110 V

1

80°C, Phosphatase

1,607,848

161,284

5,597,277

99

3,378

10.04%

 

550 V

8

80°C, Phosphatase

16,290,720

1,480,012

46,444,135

935

29,637

9.09%

 

110 V

1

80°C

214,070

48,304

1,718,507

29

991

22.58%

 

110 V

1

95°C

356,586

51,052

1,798,348

31

1,169

14.33%

TP2

110 V

1

80°C, Phosphatase

2,088,705

177,944

6,147,860

50

1,713

8.52%

 

110 V

1

80°C

216,159

53,463

1,879,011

16

560

24.74%

 

110 V

1

95°C

354,155

62,259

2,170,975

15

516

17.58%

TP2RE

110 V

1

80°C, Phosphatase

233,613

32,045

1,094,783

10

318

13.72%

 

110 V

1

80°C

213,958

59,530

2,072,120

26

928

27.84%

 

110 V

1

95°C

247,784

55,848

1,939,018

22

781

22.55%

  1. Sample TP was extracted in duplicate, and identical volumes of the extracts were tSMS sequenced on Helicos 110 FOV channels following different template preparation procedures as described in the methods section. The total number of sequences (#Seqs) as well as the number of hits mapping the horse reference nuclear (nucDNA) and mitochondrial (mtDNA) genome with mapping qualities higher than 25 but with no hit on the human reference genomes hg19 and rCRS are reported. The total sequence length covered by these reads is indicated in bp. The fraction of endogenous reads is estimated by summing the number of reads identified in nucDNA and mtDNA and dividing by the total number of reads generated per channel.