This directory contains the SNPs nuclear capture data of the 34,000 -year-old modern human found outside any archaeological context in the Salkhit Valley,Mongolia. ----------------------- Sequences from individual single stranded libraries ----------------------- Bam files containing non-aligned and aligned sequences to the human reference genome hg19 Base calling was performed using Bustard. Adapter sequences were removed and overlapping forward and reverse reads were merged using leeHom. "Sequences were aligned with BWA using parameters for ancient DNA ""-n 0.01 -o 2 -l 16500"". " LibraryID Sample Capture probe set G3549 Salkhit skullcap - A - Arcadm Panel 4 _ Archaic Admixture G3550 Salkhit skullcap - C - Arcadm Panel 4 _ Archaic Admixture G3551 Salkhit skullcap - B - Arcadm Panel 4 _ Archaic Admixture G5736 Bleached - Salkhit skullcap - A ArcAdm Panel 4 _ Archaic Admixture G5737 Bleached - Salkhit skullcap - C ArcAdm Panel 4 _ Archaic Admixture G5738 Bleached - Salkhit skullcap - B ArcAdm Panel 4 _ Archaic Admixture G5742 Bleached - Salkhit skullcap - A 1000k Panel 3_1000k G5743 Bleached - Salkhit skullcap - C 1000k Panel 3_1000k G5744 Bleached - Salkhit skullcap - B 1000k Panel 3_1000k G5746 Salkhit skullcap - A - 1000k Panel 3_1000k G5747 Salkhit skullcap - C - 1000k Panel 3_1000k G5748 Salkhit skullcap - B - 1000k Panel 3_1000k G5750 Bleached - Salkhit skullcap - A 390k Panel 1_390k G5752 Bleached - Salkhit skullcap - B 390k Panel 1_390k G5754 Salkhit skullcap - A - 390k Panel 1_390k G5755 Salkhit skullcap - C - 390k Panel 1_390k G5756 Salkhit skullcap - B - 390k Panel 1_390k G5758 Bleached - Salkhit skullcap - A 840k_sup Panel 2_840k G5760 Bleached - Salkhit skullcap - B 840k_sup Panel 2_840k G5762 Salkhit skullcap - A - 840k_sup Panel 2_840k G5763 Salkhit skullcap - C - 840k_sup Panel 2_840k G5764 Salkhit skullcap - B - 840k_sup Panel 2_840k ----------------------- Merged sequences from all libraries as used for the different analyses ----------------------- After mapping to the hg19 reference genome, sequences starting and ending at identical coordinates (representing PCR duplicates) were collapsed into a single sequence using bam-rmdup (https://bitbucket.org/ustenzel/biohazard). The data were restricted to sequences with length >= 35 and a mapping quality >= 25. Data from libraries captured with probes from Panel 1, 2 and 3 were restrictec to sequence showing evidence for cytosine to tymine mismatch at the first or last base of the sequence. LibraryID Sample Capture probe set G3549 Salkhit skullcap - A, B, C - bleached and non bleached, deaminated sequences only Panel 1,2 and 3 _ 2200k G3550 Salkhit skullcap - A, B, C - bleached and non bleached Panel 4 _ Archaic Contact: Email: diyendo_massilani@eva.mpg.de