---

type: position_score

table:
  filename: LINSIGHT.bw
#  format: tabix

  header_mode: none
  chrom_mapping:
    del_prefix: chr
  # defined by score_type
  chrom:
    index: 0
  pos_begin:
    index: 1
  pos_end:
    index: 2

# score values
scores:
  - id: LINSIGHT
    index: 3
    type: float
    desc: |
      The LINSIGHT score measures the probability of negative selection on noncoding
      sites.
    small_values_desc: "negative selection is less likely"
    large_values_desc: "negative selection is more likely"
    histogram:
      type: number
      number_of_bins: 100
      view_range:
        min: 0.0
        max: 1.0
      y_log_scale: True

default_annotation:
  - source: LINSIGHT
    name: linsight

meta:
  summary: |

    The likelihood of negative selection on noncoding sites

  description: |

    [LINSIGHT](https://github.com/CshlSiepelLab/LINSIGHT/tree/master) (Linear INSIGHT) is a computational tool designed to predict the likelihood of negative selection on noncoding nucleotide sites. It identifies noncoding sites where mutations are likely to have deleterious fitness consequences, thus playing a crucial role in phenotypic variation and disease. LINSIGHT combines a generalized linear model with a probabilistic model of molecular evolution. This integration allows it to merge functional genomic data (such as chromatin state, transcription factor binding, and other regulatory information) with evolutionary conservation data.

    [Huang et al. Fast, scalable prediction of deleterious noncoding variants from functional and population genomic data. Nature Genetics 2017.](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5395419/)

    Downloaded on: 06/07/24

    [http://compgen.cshl.edu/LINSIGHT/LINSIGHT.bw](http://compgen.cshl.edu/LINSIGHT/LINSIGHT.bw)

  labels:
    reference_genome: hg19/genomes/GATK_ResourceBundle_5777_b37_phiX174

