{
  "job": {
    "label": "Job Details",
    "value": {
      "jobpk": {
        "label": "Job ID",
        "value": "49,917",
        "description": "Job Identifier",
        "type": "integer"
      },
      "servername": {
        "label": "Server name",
        "value": "134.147.213.10",
        "description": "Name or IP of the server that ran job",
        "type": "string"
      },
      "created_at": {
        "label": "Created at",
        "value": "2022-02-21T12:24:03.514Z",
        "description": "Date job was created",
        "type": "decimal"
      },
      "fullname": {
        "label": "User Name",
        "value": "Wanda Gerding",
        "description": "Full name of user who launched job",
        "type": "string"
      },
      "operationname": {
        "label": "Job type",
        "value": "Annotated de Novo Assembly",
        "description": "The type of operation performed",
        "type": "string"
      },
      "access": {
        "label": "Access Version",
        "value": "1.7",
        "description": "Bionano Access Version",
        "type": "string"
      },
      "solve": {
        "label": "Solve Version",
        "value": "Solve3.7_10192021_74_1",
        "description": "Bionano Solve Version",
        "type": "string"
      },
      "rescale": {
        "label": "Compute On Demand Version",
        "value": "Solve3.7_10192021_74_1",
        "description": "Version of pipeline for Compute On Demand",
        "type": "string"
      },
      "objectalias": {
        "label": "Job Name",
        "value": "Recompute V1.7 S21-11D - De novo",
        "description": "Alias for Job",
        "type": "string"
      },
      "name": {
        "label": "Project Name",
        "value": "Biochemie Mueller_Gallego",
        "description": "Name of the project",
        "type": "string"
      },
      "projectkey": {
        "label": "Project Key",
        "value": "Cell lines",
        "description": "Project Identifier",
        "type": "string"
      },
      "samplename": {
        "label": "Sample Name",
        "value": "S21-11D",
        "description": "Name of the sample",
        "type": "string"
      },
      "sampleuid": {
        "label": "Sample UID",
        "value": "453bcfda-930d-11ec-986b-3cfdfe7ef3b0",
        "description": "System generated global unique identifier",
        "type": "string"
      },
      "reference": {
        "label": "Reference",
        "value": "hg19_DLE1_0kb_0labels.cmap",
        "description": "Name of the reference genome this sample was aligned to",
        "type": "string"
      },
      "inputjob1_jobpk": {
        "label": "Input job 1 - Job ID",
        "value": "49,913",
        "description": "Job Identifier",
        "type": "integer"
      },
      "inputjob1_objectalias": {
        "label": "Input job 1 - Job Name",
        "value": "11_2021_18_11_2021, 7CICFC6NPNAVZNWU, F2P1, 2021-11-19 23:16:20",
        "description": "Alias for Job",
        "type": "string"
      },
      "inputjob1_operationname": {
        "label": "Input job 1 - Job type",
        "value": "Copy Molecules",
        "description": "The type of operation performed",
        "type": "string"
      }
    },
    "type": "section"
  },
  "Molecule Stats (/home/bionano/access/local/jobs/49917/output/all.bnx)": {
    "label": "Molecule Stats (/home/bionano/access/local/jobs/49917/output/all.bnx)",
    "value": {
      "Total number of molecules": {
        "label": "Total number of molecules",
        "value": "952,596",
        "type": "string",
        "units": "",
        "description": "The number of molecules present in the .bnx file."
      },
      "Total length (Mbp)": {
        "label": "Total length",
        "value": "276,643.6 Mbp",
        "type": "string",
        "units": "Mbp",
        "description": "The summed length of all molecules in the bnx files."
      },
      "Average length (kbp)": {
        "label": "Average length",
        "value": "290.41 kbp",
        "type": "string",
        "units": "kbp",
        "description": "The average (mean) length of the molecules."
      },
      "Molecule N50 (kbp)": {
        "label": "Molecule N50",
        "value": "304.88 kbp",
        "type": "string",
        "units": "kbp",
        "description": "N50 can be described as a weighted median statistic such that 50% of the summed molecule length is contained in molecules equal to or larger than this value"
      },
      "Label density (/100kb)": {
        "label": "Label density",
        "value": "16.07 /100kb",
        "type": "string",
        "units": "/100kb",
        "description": "The average number of labels detected per 100 kbp of molecule length."
      }
    },
    "type": "section"
  },
  "Input molecule stats (unfiltered)": {
    "label": "Input molecule stats (unfiltered)",
    "value": {},
    "type": "section"
  },
  "Input molecule stats (filtered)": {
    "label": "Input molecule stats (filtered)",
    "value": {
      "Total number of molecules": {
        "label": "Total number of molecules",
        "value": "899,848",
        "type": "string",
        "units": "",
        "description": "The number of molecules present in the .bnx file."
      },
      "Total length (Mbp)": {
        "label": "Total length",
        "value": "263,803.76 Mbp",
        "type": "string",
        "units": "Mbp",
        "description": "The summed length of all molecules in the bnx files."
      },
      "Average length (kbp)": {
        "label": "Average length",
        "value": "293.17 kbp",
        "type": "string",
        "units": "kbp",
        "description": "The average (mean) length of the molecules."
      },
      "Molecule N50 (kbp)": {
        "label": "Molecule N50",
        "value": "307.76 kbp",
        "type": "string",
        "units": "kbp",
        "description": "N50 can be described as a weighted median statistic such that 50% of the summed molecule length is contained in molecules equal to or larger than this value"
      },
      "Label density (/100kb)": {
        "label": "Label density",
        "value": "16.31 /100kb",
        "type": "string",
        "units": "/100kb",
        "description": "The average number of labels detected per 100 kbp of molecule length."
      },
      "Coverage of the reference (X)": {
        "label": "Coverage of the reference",
        "value": "85.22 X",
        "type": "string",
        "units": "X",
        "description": "The average depth of coverage of the genome as calculated by dividing the total length of molecules by the length of the reference. Reference must be provided."
      }
    },
    "type": "section"
  },
  "Molecules aligned to the reference": {
    "label": "Molecules aligned to the reference",
    "value": {
      "Total number of molecules aligned": {
        "label": "Total number of molecules aligned",
        "value": "841,900",
        "type": "string",
        "units": "",
        "description": "The number of molecules after filtering (≥ 150 kbp) that align either to the reference file (.cmap), (e.g. GRCh37 or GRCh38) or the assembly."
      },
      "Fraction of molecules aligned": {
        "label": "Fraction of molecules aligned",
        "value": "0.94",
        "type": "string",
        "units": "",
        "description": "The proportion of filtered molecules that align to the reference or consensus genome maps (assembly only)."
      },
      "Effective coverage of reference (X)": {
        "label": "Effective coverage of reference",
        "value": "72.24 X",
        "type": "string",
        "units": "X",
        "description": "The total length of molecules divided by the length of the reference or consensus assembled maps after de novo assembly."
      },
      "Average confidence": {
        "label": "Average confidence",
        "value": "41",
        "type": "string",
        "units": "",
        "description": "The average alignment score for all the molecules that align to the reference  or assembly."
      }
    },
    "type": "section"
  },
  "De novo assembly": {
    "label": "De novo assembly",
    "value": {
      "Diploid genome map count": {
        "label": "Diploid genome map count",
        "value": "569",
        "type": "string",
        "units": "",
        "description": "The total number of assembled genome maps (.cmaps) created after the assembly process. In NGS terms, this would be referred to as contig number. The lower the number of genome maps, the higher the contiguity of your assembly."
      },
      "Diploid genome map length   (Mbp)": {
        "label": "Diploid genome map length",
        "value": "5,962.43 Mbp",
        "type": "string",
        "units": "Mbp",
        "description": "The total length of the genome assembled"
      },
      "Diploid genome map N50      (Mbp)": {
        "label": "Diploid genome map N50",
        "value": "69.55 kbp",
        "type": "string",
        "units": "kbp",
        "description": "N50 can be described as a weighted median statistic such that 50% of the summed molecule length is contained in molecules equal to or larger than this value"
      },
      "Haploid genome map count": {
        "label": "Haploid genome map count",
        "value": "338",
        "type": "string",
        "units": "",
        "description": "The total number of assembled genome maps (.cmaps) created after the assembly process. In NGS terms, this would be referred to as contig number. The lower the number of genome maps, the higher the contiguity of your assembly."
      },
      "Haploid genome map length   (Mbp)": {
        "label": "Haploid genome map length ",
        "value": "3,161.13 Mbp",
        "type": "string",
        "units": "Mbp",
        "description": "The summed length of the assembled genome maps."
      },
      "Haploid genome map N50      (Mbp)": {
        "label": "Haploid genome map N50",
        "value": "62.85 kbp",
        "type": "string",
        "units": "kbp",
        "description": "The N50 (the point of half of the mass of the distribution) of the assembled genome maps in the assembly."
      },
      "Total reference length      (Mbp)": {
        "label": "Total reference length",
        "value": "3,095.68 Mbp",
        "type": "string",
        "units": "Mbp",
        "description": "The summed length of the chromosomes (or other maps) in the specified reference."
      },
      "Total number of genome maps aligned (Fraction)": {
        "label": "Total number of genome maps aligned (Fraction)",
        "value": "457 (0.80)",
        "type": "string",
        "units": "",
        "description": "Number (and fraction) of maps that align completely or partially to the reference."
      },
      "Total unique aligned length (Mbp)": {
        "label": "Total unique aligned length",
        "value": "2,846.92 Mbp",
        "type": "string",
        "units": "Mbp",
        "description": "The summed aligned length of the reference. This can be thought of as the amount of the reference “covered.”"
      },
      "Total unique aligned length / reference length": {
        "label": "Total unique aligned length / reference length",
        "value": "0.92 %",
        "type": "string",
        "units": "%",
        "description": "The percentage of the reference length covered by the unique aligned length.”"
      }
    },
    "type": "section"
  },
  "Molecules aligned to the assembly": {
    "label": "Molecules aligned to the assembly",
    "value": {
      "Total number of molecules aligned": {
        "label": "Total number of molecules aligned",
        "value": "852,210",
        "type": "string",
        "units": "",
        "description": "The number of molecules after filtering (≥ 150 kbp) that align either to the reference file (.cmap), (e.g. GRCh37 or GRCh38) or the assembly."
      },
      "Effective coverage of  assembly (X)": {
        "label": "Effective coverage of  assembly",
        "value": "47.92 X",
        "type": "string",
        "units": "X",
        "description": "The total length of filtered (≥ 150 kbp) and aligned molecules divided by the length of the reference or consensus assembled maps after de novo assembly."
      },
      "Average confidence": {
        "label": "Average confidence",
        "value": "56.6",
        "type": "string",
        "units": "",
        "description": "The average alignment score for all the molecules that align to the reference  or assembly."
      }
    },
    "type": "section"
  },
  "SV summary (clustered counts)": {
    "label": "SV summary (clustered counts)",
    "value": {
      "Deletions": {
        "label": "Deletions",
        "value": "1,408",
        "type": "string",
        "units": "",
        "description": "The number of segments in the genome map assembly which are shorter when compared to the reference, indicating that a deletion occurred in the segment."
      },
      "Insertions": {
        "label": "Insertions",
        "value": "2,926",
        "type": "string",
        "units": "",
        "description": "The number of segments in the genome map assembly which are longer when compared to the reference, indicating that an insertion occurred in the segment."
      },
      "Duplications": {
        "label": "Duplications",
        "value": "70",
        "type": "string",
        "units": "",
        "description": "The number of nonredundant segmental tandem and tandem-inverted duplication patterns found in the genome map assembly compared to the reference."
      },
      "Inversion breakpoints": {
        "label": "Inversion breakpoints",
        "value": "57",
        "type": "string",
        "units": "",
        "description": "The number of inversion breakpoints found in the genome map assembly compared to the reference based on the observation that patterns are in opposite orientation compared to adjacent sequence patterns."
      },
      "Interchr. translocation breakpoints": {
        "label": "Interchr. translocation breakpoints",
        "value": "0",
        "type": "string",
        "units": "",
        "description": "The number of nonredundant interchromosomal translocation breakpoints resulting in fusion between different chromosomes in the genome map assembly compared to the reference."
      },
      "Intrachr. translocation breakpoints": {
        "label": "Intrachr. fusion breakpoints",
        "value": "0",
        "type": "string",
        "units": "",
        "description": "The number of translocation breakpoints within a chromosome in the genome map assembly compared to the reference"
      }
    },
    "type": "section"
  },
  "AOH/LOH Detection Stats": {
    "label": "AOH/LOH Detection Stats",
    "value": {
      "Total number of calls in autosome": {
        "label": "Total number of calls in autosome",
        "value": "4",
        "type": "string",
        "units": "",
        "description": "Total number of regions in the autosome identified as a having absence or loss or heterozygosity (AOH/LOH)."
      },
      "Total number of calls greater than 25 Mbp in autosome": {
        "label": "Total number of calls greater than 25 Mbp in autosome",
        "value": "0",
        "type": "string",
        "units": "",
        "description": "Total number of regions greater than 25 Mbp in the autosome identified as a having absence or loss or heterozygosity (AOH/LOH)."
      },
      "Total number of calls greater than 40 Mbp in autosome": {
        "label": "Total number of calls greater than 40 Mbp in autosome",
        "value": "0",
        "type": "string",
        "units": "",
        "description": "Total number of regions greater than 40 Mbp in the autosome identified as a having absence or loss or heterozygosity (AOH/LOH). Large calls are higher confidence calls."
      },
      "Fraction of autosome called as AOH/LOH": {
        "label": "Fraction of autosome called as AOH/LOH",
        "value": "0.0033",
        "type": "string",
        "units": "",
        "description": "Total fraction of the autosome identified as a having absence or loss or heterozygosity (AOH/LOH); high values may indicate consanguinity."
      }
    },
    "type": "section"
  },
  "CNV Statistics": {
    "label": "CNV Statistics",
    "value": {
      "Version": {
        "label": "Version",
        "value": "3ba3c0ad741221ae39d5203b0fc304f2cc1dd599; installed on 2021-10-11 23:53:37",
        "type": "string"
      },
      "Sex": {
        "label": "Sex",
        "value": "male",
        "type": "string",
        "description": "Sex determined based on coverage of sex chromosomes"
      },
      "Median Coverage": {
        "label": "Median Coverage",
        "value": "83",
        "type": "string",
        "description": "Median number of molecules covering each position genome-wide"
      },
      "Global coefficient of variation": {
        "label": "Global coefficient of variation",
        "value": "0.14",
        "type": "string",
        "description": "Coefficient of variation in coverage genome-wide"
      },
      "Median local coefficient of variation (2Mbp)": {
        "label": "Median local coefficient of variation (2Mbp)",
        "value": "0.11",
        "type": "string",
        "description": "Median coefficient of variation observed within 2Mbp intervals"
      },
      "Percent above expected (2 Mbp window)": {
        "label": "Percent above expected (2 Mbp window)",
        "value": "-3.3",
        "type": "string",
        "description": "Percent difference between the expected coefficient of variation in sample with low systematic biases (2 Mbp windows) and the observed coefficient of variation in the sample. If the observed percent different is greater than 20%, the sample should be considered to contain systematic bias."
      },
      "Median local coefficient of variation (6Mbp)": {
        "label": "Median local coefficient of variation (6Mbp)",
        "value": "0.12",
        "type": "string",
        "description": "Median coefficient of variation observed within 6Mbp intervals"
      },
      "Percent above expected (6 Mbp window)": {
        "label": "Percent above expected (6 Mbp window)",
        "value": "10.19",
        "type": "string",
        "description": "Percent difference between the expected coefficient of variation in sample with low systematic biases (6 Mbp windows) and the observed coefficient of variation in the sample. If the observed percent different is greater than 20%, the sample should be considered to contain systematic bias."
      },
      "Correlation with label density": {
        "label": "Correlation with label density",
        "value": "-0.09",
        "type": "string",
        "description": "Correlation between coverage of genomic regions and the label density in the given regions. Value greater than 0.25 indicates high systematic biases and sample may have more false positive CNV calls."
      },
      "Wave template correlation": {
        "label": "Wave template correlation",
        "value": "0",
        "type": "string",
        "description": "Correlation between the coverage of the query sample and the coverage profiles from known samples with large systematic bias. Value greater than 0.4 indicates high systematic biases and sample may have more false positive CNV calls."
      }
    },
    "type": "section"
  }
}