What are the definitions of the Deep Sequence QC metrics in the Arima SV pipeline?
HiC QC: If % INTRA > 15kb is > 25% a sample passes HiC QC
SV QC: If the % INTRA > 15kb is > 25% and the Lcis/trans ratio is > 1 a samples passes SV QC
Sample Name: Sample name
Raw PE reads: Raw # of read pairs
Mapped SE reads: # of single-end reads that can be mapped to the reference
%_Mapped SE_reads: % of single-end reads that can be mapped to the reference, out of total # of single-end reads
Duplicates: # of duplicated read pairs
% Duplicates: % of duplicated read pairs, out of all read pairs
Unique valid pairs: HiC read pairs which are not derived from artifacts such as self-circles and dangling-ends, and which contain spatial proximity information
%Unique valid pairs: % of unique valid read pairs, out of all read pairs
Library Complexity: Theoretical # of unique molecules in a Hi-C library.
INTRA pairs: All unique pairs where both read-ends align to the same chromosome
% INTRA pairs: % of all unique total pairs that have both read-ends aligning to the same chromosome
INTRA >15kb pairs(Lcis): All unique pairs where both read-ends align to the same chromosome and have an insert size >=15kb
% INTRA >15kb pairs(Lcis): Intra_ge_15kb_pairs: % of all unique total pairs that have both read-ends aligning to the same chromosome and have an insert size >=15kb
INTER pairs(Trans): All unique pairs where each read-end aligns to a different chromosome
Lcis_trans_ratio: The ratio of Lcis to Trans data. This is the signal to noise ratio for translocation calling.
