General Description
Contained in this directory is the data corresponding to SI 18 of the High Coverage Altai Neandertal manuscript (Pruefer et al. 2013)
There are two directories, one containing the Human catalog (derived changes on the human lineage) and one the Archaic catalog (changes on the archaic lineage)
Within each directory are the full set of single nucleotide changes (*SNC*) and insertion/deletions (*InDel*)
The sub-directories EnsemblGenes and CCDS provide the subset of the catalogs corresponding to changes in Ensembl genes and changes in CCDS genes respectively.
 

/HumanCatalog:
HumanDerived_SNC_bothgq30.all_combined_maxsco_ranked.tsv        The full set of SNCs in the human catalog
HumanDerived_InDel_bothgq30.all_combined_maxsco_ranked.tsv	The full set of InDels in the human catalog

/HumanCatalog/CCDS:
HumanDerived_SNC_ccds_3utr.tsv	SNCs in the 3' UTRs of CCDS genes
HumanDerived_SNC_ccds_5utr.tsv	SNCs in the 5' UTRs of CCDS genes
HumanDerived_SNC_ccds_nonsynonymous.tsv	Nonsynonymous substitutions in CCDS genes
HumanDerived_SNC_ccds_splice.tsv	Substitutions in splice sites of CCDS genes
HumanDerived_SNC_ccds_synonymous.tsv	Synonymous substitutions in CCDS genes

/HumanCatalog/EnsemblGenes:
HumanDerived_SNC_3utr.tsv	SNCs in the 3' UTRs of Ensembl genes
HumanDerived_SNC_5utr.tsv	SNCs in the 5' UTRs of Ensembl genes
HumanDerived_SNC_nonsynonymous.tsv	Nonsynonymous substitutions in Ensembl genes
HumanDerived_SNC_splice.tsv	Substitutions in splice sites of Ensembl genes
HumanDerived_SNC_synonymous.tsv	 Synonymous substitutions in Ensembl genes



ArchaicCatalog/:
ArchaicDerived_SNC_bothgq30.all_combined_maxsco_ranked.tsv      The full set of SNCs in the Archaic Catalog
ArchaicDerived_Indel_bothgq30.all_combined_maxsco_ranked.tsv	The full set of InDels in the Archaic Catalog

ArchaicCataloCCDS:
ArchaicDerived_SNC_ccds_3utr.tsv	SNCs in the 3' UTRs of CCDS genes
ArchaicDerived_SNC_ccds_5utr.tsv	SNCs in the 5' UTRs of CCDS genes
ArchaicDerived_SNC_ccds_nonsynonymous.tsv	Nonsynonymous substitutions in CCDS genes
ArchaicDerived_SNC_ccds_splice.tsv	Substitutions in splice sites of CCDS genes
ArchaicDerived_SNC_ccds_synonymous.tsv	Synonymous substitutions in CCDS genes

ArchaicCatalog/EnsemblGenes:
ArchaicDerived_SNC_3utr.tsv	SNCs in the 3' UTRs of Ensembl genes
ArchaicDerived_SNC_5utr.tsv	SNCs in the 5' UTRs of Ensembl genes
ArchaicDerived_SNC_nonsynonymous.tsv	Nonsynonymous substitutions in Ensembl genes
ArchaicDerived_SNC_splice.tsv	Substitutions in splice sites of Ensembl genes
ArchaicDerived_SNC_synonymous.tsv	Synonymous substitutions in Ensembl genes