Quantifying and reducing spurious alignments for the analysis of ultra-short ancient DNA sequences

Table 1 Mezmaiskaya and Sima de los Huesos (SH) sequence length cutoffs allowing for less than 1% or 10% spurious alignments

Samples	Hominin DNA (%)^a	Length cutoff (bp)^b		Total number of hominin bases recovered (Mbp)			Fold change
Samples	Hominin DNA (%)^a	L _1%	L _10%	35 bp	L _1%	L _10%	L_1%/35 bp	L_10%/35 bp
Mezmaiskaya 1	8.84	22	20	88.53	121.17	121.73	1.37	1.37
SH Femur frag.	0.11	32	29	0.81	1.14	1.52	1.41	1.88
SH Incisor	0.18	34	27	1.49	1.70	3.71	1.14	2.49
SH Molar	0.03	35	30	0.13	0.13	0.25	1.00	1.98
SH FemurXIII	0.02	46	34	0.15	0.03	0.18	0.23	1.17

^aThe percentage of endogenous hominin DNA was calculated as the fraction of sequences of at least 35 bp that mapped to the human reference over the total number of sequences
^bThe values L_1% and L_10% refer to length cutoffs that limit the fraction of spurious alignment to under 1% and 10%, respectively. Column 35 bp refers to the standard 35-bp length threshold. Values have been computed using sequences with terminal C-to-T changes only and disregarding sequences with indels

ISSN: 1741-7007