Table 1.

Overview of the data and results

Sample	Trimmed reads	Plague reads	Normalized plague reads	Normalized Kraken reads	Damage C→T	Human DNA %	mtDNA haplogroup
Negative_cementum	12,326,411	77	62	1		22.3
Negative_petrous	10,561,575	32	30	0		31.0
Rise00_dentine	11,967,447	9	8	0		0.1
Rise00_cementum	22,058,165	28	13	0		2.3	H5a1
Rise00_petrous	16,417,368	1	1	0		62.0	H5a1
Rise386_dentine	17,899,720	1,243	694	45	0.08	39.6	J1c1
Rise386_cementum	19,911,365	205	103	5	0.11	65.9	J1c1b1a
Rise386_petrous	23,943,845	3	1	0		68.8	J1c1b1a
Rise397_dentine	15,354,984	33	21	0		0.1
Rise397_cementum	15,791,765	371	235	16	0.24	3.5
Rise397_petrous	12,583,231	6	5	0		7.5
Rise509_dentine	20,558,557	11,822	5,750	394	0.16	48.5	T2c1a2
Rise509_cementum	16,402,996	1,412	861	62	0.14	77.5	T2c1a2
Rise509_petrous	21,077,122	7	3	0		58.7	T2c1a2
Rise511_dentine	12,107,391	2,799	2,312	138	0.15	23.0	J2a2a
Rise511_cementum	19,841,683	1,384	698	56	0.14	31.8	J2a2a

Trimmed reads, total number of DNA reads per DNA library after adapter trimming, except for the negative control samples which are average values of 10 samples; Plague reads and Normalized plague reads, observed and normalized number of reads identified as Y. pestis based on reference genome mapping; Normalized Kraken reads, normalized number of reads identified as Y. pestis with the Kraken approach (Wood & Salzberg, 2014); Damage C→T, observed frequency of C→T transitions at the first position at the 5′ end of the mapped reads relative to the reference genome of Y. pestis; Human DNA %, the endogenous human DNA content; mtDNA haplogroup, the human mitochondrial haplogroup identified with haplogrep (Weissensteiner et al., 2016) in samples with sufficient data. Normalizations are based on mapped fractions assuming 10 million trimmed reads.