--- title: What are the definitions of the Deep Sequence QC metrics in the Arima SV pipeline? description: What are the definitions of the Deep Sequence QC metrics in the Arima SV pipeline? --- [Skip to content](https://support.arimagenomics.com/migration/what-are-the-definitions-of-the-deep-sequence-qc-metrics-in-the-arima-sv-pipeline#main-content) English Show submenu for translations ![](https://support.arimagenomics.com/hs-fs/hubfs/ArimaGenomics_Logo_White_Large_150dpi.png?width=100&height=75&name=ArimaGenomics_Logo_White_Large_150dpi.png) - [Services](https://support.arimagenomics.com/migration/what-are-the-definitions-of-the-deep-sequence-qc-metrics-in-the-arima-sv-pipeline#services) - [Blog](https://support.arimagenomics.com/migration/what-are-the-definitions-of-the-deep-sequence-qc-metrics-in-the-arima-sv-pipeline#blog) - [Gallery](https://support.arimagenomics.com/migration/what-are-the-definitions-of-the-deep-sequence-qc-metrics-in-the-arima-sv-pipeline#gallery) - [About](https://support.arimagenomics.com/migration/what-are-the-definitions-of-the-deep-sequence-qc-metrics-in-the-arima-sv-pipeline#about) Open main navigation Close main navigation - [Services](https://support.arimagenomics.com/migration/what-are-the-definitions-of-the-deep-sequence-qc-metrics-in-the-arima-sv-pipeline#services) - [Blog](https://support.arimagenomics.com/migration/what-are-the-definitions-of-the-deep-sequence-qc-metrics-in-the-arima-sv-pipeline#blog) - [Gallery](https://support.arimagenomics.com/migration/what-are-the-definitions-of-the-deep-sequence-qc-metrics-in-the-arima-sv-pipeline#gallery) - [About](https://support.arimagenomics.com/migration/what-are-the-definitions-of-the-deep-sequence-qc-metrics-in-the-arima-sv-pipeline#about) - English Show submenu for translations - Contact us Contact us How can we help you? - There are no suggestions because the search field is empty. 1. [Help Center](https://support.arimagenomics.com/migration/?hsLang=en) 2. [SV Pipeline FAQ](https://support.arimagenomics.com/migration//sv-pipeline-faq?hsLang=en) # 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. - **SVs:** # of SV calls made by the Arima SV Pipeline - [SV Pipeline FAQ](https://support.arimagenomics.com/migration//sv-pipeline-faq?hsLang=en) - [QC Pipeline FAQ](https://support.arimagenomics.com/migration//qc-pipeline-faq?hsLang=en) - [General Portal FAQ](https://support.arimagenomics.com/migration//general-portal-faq?hsLang=en) - [Services](https://support.arimagenomics.com/migration/what-are-the-definitions-of-the-deep-sequence-qc-metrics-in-the-arima-sv-pipeline#services) - [Blog](https://support.arimagenomics.com/migration/what-are-the-definitions-of-the-deep-sequence-qc-metrics-in-the-arima-sv-pipeline#blog) - [Gallery](https://support.arimagenomics.com/migration/what-are-the-definitions-of-the-deep-sequence-qc-metrics-in-the-arima-sv-pipeline#gallery) - [About](https://support.arimagenomics.com/migration/what-are-the-definitions-of-the-deep-sequence-qc-metrics-in-the-arima-sv-pipeline#about) [![Chill listening crop-3](https://support.arimagenomics.com/hs-fs/hubfs/ArimaGenomics_Logo_FullColor_Web_600x193px.png?width=170&height=55&name=ArimaGenomics_Logo_FullColor_Web_600x193px.png "Chill listening crop-3")](http://arimagenomics.com) [mailto:email@email.com](mailto:email@email.com) Copyright © 2026, Arima Genomics