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