{
  "Comment": "See AssemblySummary.html for a human-readable version of this file",
  "Shasta version": "Shasta Release 0.11.1",
  "Reads used in this assembly":
  {
    "Read representation": "1 (RLE)",
    "Minimum read length": 200,
    "Number of reads": 1706664,
    "Number of read bases": 5560477726,
    "Average read length": 3258,
    "Read N50": 5563,
    "Number of run-length encoded bases": 3890327243,
    "Average length ratio of run-length encoded sequence over raw sequence": 0.6996,
    "Number of reads flagged as palindromic by self alignment": 119421,
    "Number of reads flagged as chimeric": 621
  },
  "Reads discarded on input":
  {
    "Reads discarded on input because they contained invalid bases":
    {
      "Reads": 0,
      "Bases": 0
    },
    "Reads discarded on input because they were too short":
    {
      "Reads": 1871,
      "Bases": 250931
    },
    "Reads discarded on input because they contained repeat counts greater than 255":
    {
      "Reads": 72,
      "Bases": 322361
    },
    "Reads discarded on input, total":
    {
      "Reads": 1943,
      "Bases": 573292
    },
    "Fraction of reads discarded on input over total present in input files":
    {
      "Reads": 0.001137,
      "Bases": 0.0001031
    }
  },
  "Marker k-mers":
  {
    "Length k of k-mers used as markers": 14,
    "Total number of k-mers": 6377292,
    "Number of k-mers used as markers": 638031,
    "Fraction of k<-mers used as markers": 0.1  },
  "Markers":
  {
    "Total number of markers on all reads, one strand": 379210669,
    "Total number of markers on all reads, both strands": 758421338,
    "Average number of markers per raw base": 0.0682,
    "Average number of markers per run-length encoded base": 0.09748,
    "Average base offset between markers in raw sequence": 14.66,
    "Average base offset between markers in run-length encoded sequence": 10.26,
    "Average base gap between markers in run-length encoded sequence": -3.741
  },
  "Alignments":
  {
    "Number of alignment candidates found by the LowHash algorithm": 40390,
    "Number of good alignments": 36638,
    "Number of good alignments kept in the read graph": 27757
  },
  "Alignment criteria actually used for creation of the read graph":
  {
    "minAlignedMarkerCount": 25,
    "minAlignedFraction": 0.475,
    "maxSkip": 21,
    "maxDrift": 10,
    "maxTrim": 80
  },
  "Read graph":
  {
    "Number of vertices": 3413328,
    "Number of edges": 55514,
    "Isolated reads":
    {
      "Reads": 1678505,
      "Bases": 5365926349
    },
    "Non-isolated reads":
    {
      "Reads": 28159,
      "Bases": 194551377
    },
    "Isolated reads fraction":
    {
      "Reads": 0.9835,
      "Bases": 0.965
    },
    "Non-isolated reads fraction":
    {
      "Reads": 0.0165,
      "Bases": 0.03499
    }
  },
  "Marker graph":
  {
    "Total number of vertices": 222694,
    "Total number of edges": 302514,
    "Number of vertices that are not isolated after edge removal": 201106,
    "Number of edges that were not removed": 199368
  },
  "Assembly graph":
  {
    "Number of vertices": 3502,
    "Number of edges": 1764,
    "Number of edges assembled": 882
  },
  "Assembled segments":
  {
    "Number of segments assembled": 882,
    "Total assembled segment length": 2444894,
    "Longest assembled segment length": 10877,
    "Assembled segments N50": 4170
  },
  "Performance":
  {
    "Elapsed time (seconds)": 240.9,
    "Elapsed time (minutes)": 4.014,
    "Elapsed time (hours)": 0.0669,
    "Average CPU utilization": 0.204,
    "Peak memory utilization (bytes)": 37619863552,
    "Number of threads used": 60,
    "Total number of virtual CPUs available": 20,
    "Total physical memory available (bytes)": 270208720896
  }
}