Table 1.

tSMS sequencing of ancient DNA extracts from sample CA (>50,300BP)

Sample	Platform	#	Conditions	#Seqs	nucDNA	bp	mtDNA	bp	%Endo.
CA1	1100 V	1	Spiking	4,559,011*	57,946	1,728,020	3	107	1.27%
	1100 V	1	80°C	787,255	29,837	896,617	11	365	3.79%
	1100 V	1	95°C	35,055	1,020	27,242	0	0	2.91%
CA2	1100 V	1	Spiking	4,888,026*	54,266	1,599,775	3	90	1.11%
	1100 V	1	80°C	730,418	55,546	1,717,054	12	385	7.61%
	1100 V	1	95°C	51,550	1,231	33,023	0	0	2.39%

Sample CA was extracted in duplicate (CA1 and CA2), and identical volumes of the extracts were tSMS sequenced on a Helicos 1100 FOV platform following different template preparation procedures as described in the methods section. The total number of sequences without (#Seqs) and with (*) filtering for oligonucleotides used for spiking, 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 (minus reads corresponding to spiking oligonucleotides in the specific case of spiking experiments).