This directory contains the BAM files and VCF files used for analysis in "Genetic insights into the social organization of Neanderthals" (Skov et al 2022). ------------------------------ BAMS ------------------------------ The bam files are merged by individual and specimen. For individuals we report the merged data sets made from all curated reads. For specimens we provide all sequences (all_seq), sequences with evidence of deamination in the first/last 3 basepairs and a list of curated sequences (all libraries with less than 2% contamination) - see SI section 3,4,5 in Skov et al for further details. The BAM files are provided for the mitochondria, y chromosome for males and the nuclear capture. The Y chromosome and nuclear data are mapped against hg19 and the mitochondria sequences are mapped against the concensus sequence of Chagyrskaya 8 from Mafessoni et al 2020. ------------------------------ RAW_BAMS ------------------------------ In the RAW_BAMS we provide all reads in BAM format (including unmapped) for all 17 Chagyrskaya and 10 Okladnikov remains (note that only 15 from Chagyrskaya and 2 from Okladnikov contained ancient DNA are were analysed in the paper). The read pairs with overlapping ends were merged into one sequence (leeHom). The reads are grouped by specimen. The name of the files contain the following information: {target}.{indexed_libraryID}.{sequenceing_runID}.{lane}.bam Where target can be either: - mtDNA capture (rCRs_mtDNA, mt) - steffi_504plus4 (nuclear capture using an array based on 504 modern humans and 4 archaics) - shotgun sequencing (shotgun) - Ychromosome6.9M (6.9 Mb capture of the Y chromosome) ------------------------------ VCF ------------------------------ > NuclearTargetSites.bed 643,472 tranvsertions sites from the Array (see SI 5 - these numbers are AFTER removing sites with too high coverage and removing sites that are close to other sites) SNPs with derived allele frequency > 10% (AFR_high n=400,471) SNPs uniformly sampled from 2%-frequency-bins (AFR_uni n=188,905) SNPs varying among the four archaic genomes (ARC_var n=272,035) Fixed differences between archaics and Africans (ARC_fix n=11,047) Sites fixed derived in archaics, while not fixed derived in Africans (ARC_fixdev n=82,922) > 12Chagyrskaya_2Okladnikov_pseudohaploid.vcf The genotypes are pseudohaploid and converted into either homozygous ref/alternative for the 12 Chagyrskaya individuals and the 2 Okladnikovs. > 31samples_pseudohaploid.vcf The genotypes are pseudohaploid and converted into either homozygous ref/alternative for the 3 modern humans, 4 high coverage archaics (Altai, Vindija, Chagyrskaya and Denisova), 10 low coverage archaics (only deaminated reads are sampled), 12 Chagyrskaya individuals and the 2 Okladnikovs. > Ychrom.vcf Genotypes for 1 Chimpanzee, 3 modern humans, 2 Denisovans, 7 Chagyrskaya individuals, 1 Okladnikov individual and 3 previously published Neanderthals > YchromINFO.xlsx Same info as in Ychrom but as an excel file ------------------------------ mtDNA_FASTA ------------------------------ This directory contains a multiple alignment of the cambridge reference (rcrs), 54 modern humans, 25 neanderthals, 4 denisovans, 1 individual from sima de los huesos, 1 chimpanzee, 1 sediment sample from chagyrskaya cave, 15 chagyrskaya SPECIMENS (you can remove chagyrskaya6, chagyrskaya63 and chagyrskaya13 to keep one sequence from each individual) and 2 okladnikov individuals. There is also a directory with the concensus sequence for each specimen (Specimens). All data is made freely available. Contact: Laurits Skov lauritsskov2@gmail.com