{
   "orders" : {
      "DCas18-3587" : {
         "clientemail" : "eder.oliveira@embrapa.br",
         "sequencing" : {
            "1" : {
               "HiSeq 2500" : "2018-07-12 19:12:47"
            }
         },
         "orderdatetime" : "2018-06-20 03:03:30",
         "clientname" : "Dr. Eder Oliveira",
         "productname" : "Cassava DArTseqLD (1.0)"
      }
   },
   "errormsg" : "OK",
   "error" : 0,
   "datafiles" : {
      "Report_DCas18-3587_SNP_2.csv" : {
         "filetype" : "SNP",
         "exportdetails" : {
            "metacolsdetails" : {
               "SNP" : "In 2 rows format: this column is blank in the Reference row, and contains the base position and base variant details in the SNP row. In 1 row format: contains the base position and base variant details",
               "FreqHomSnp" : "The proportion of samples which score as homozygous for the SNP allele",
               "CallRate" : "The proportion of samples for which the genotype call is either \"1\" or \"0\", rather than \"-\" ",
               "AlleleSequence" : "In 1 row format: the sequence of the Reference allele. In 2 rows format: the sequence of the Reference allele is in the Ref row, the sequence of the SNP allele in the SNP row",
               "TrimmedSequence" : "Same as the full sequence, but with removed adapters in short marker tags",
               "OneRatioRef" : "The proportion of samples for which the genotype score is \"1\", in the Reference allele row",
               "AvgCountRef" : "The sum of the tag read counts for all samples, divided by the number of samples with non-zero tag read counts, for the Reference allele row",
               "FreqHets" : "The proportion of samples which score as heterozygous.",
               "AvgCountSnp" : "The sum of the tag read counts for all samples, divided by the number of samples with non-zero tag read counts, for the SNP allele row",
               "AlleleID" : "Unique identifier for the sequence in which the SNP marker occurs",
               "AvgPIC" : "The average of the polymorphism information content (PIC) of the Reference and SNP allele rows",
               "RepAvg" : "The proportion of technical replicate assay pairs for which the marker score is consistent",
               "FreqHomRef" : "The proportion of samples which score as homozygous for the Reference allele",
               "PICSnp" : "The polymorphism information content (PIC) for the SNP allele row",
               "PICRef" : "The polymorphism information content (PIC) for the Reference allele row",
               "SnpPosition" : "The position (zero indexed) in the sequence tag at which the defined SNP variant base occurs",
               "OneRatioSnp" : "The proportion of samples for which the genotype score is \"1\", in the SNP allele row"
            },
            "headerrowsnumber" : 7,
            "lastdatacol" : 2007,
            "notdescribedmetacolumns" : 0,
            "idcolposition" : 1,
            "firstdatacol" : 22,
            "alncoldetails" : {
               "Chrom_" : "Contig(s) with the best alignment of marker / tag to an existing model genome",
               "AlnEvalue_" : "E value of the best alignment to an existing model genome",
               "ChromPos_" : "Position(s) on contig(s) with the best alignment of marker / tag to an existing model genome",
               "AlnCnt_" : "Total count of aligning markers / tags with selection criteria described below"
            },
            "metacolspositions" : [
               "2",
               "3",
               "4",
               "5",
               "6",
               "7",
               "8",
               "9",
               "10",
               "11",
               "12",
               "13",
               "14",
               "15",
               "16",
               "17",
               "18",
               "19",
               "20",
               "21"
            ],
            "headerrowsdescr" : {
               "6" : "genotype name",
               "4" : "well column position",
               "1" : "DArT plate barcode",
               "3" : "well row position",
               "0" : "Order number where sample belongs to - important for multi-orders reports",
               "2" : "client plate barcode",
               "5" : "sample comments"
            },
            "modelreferences" : {
               "Cassava_v61" : ""
            }
         },
         "description" : "SNP 2 Rows Format: Each allele scored in a binary fashion (\"1\"=Presence and \"0\"=Absence). Heterozygotes are therefore scored as 1/1 (presence for both alleles/both rows)",
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         "exportdetails" : {
            "metacolsdetails" : {
               "Reproducibility" : "The proportion of technical replicate assay pairs for which the marker score is consistent",
               "Qpmr" : "The average of the normalized non-zero tag read counts divided by the standard deviation of the normalized non-zero tag read counts (If standard deviation is zero or near zero, the Qpmr value will be 100).",
               "PIC" : "Polymorphism Information Content",
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               "OneRatio" : "The proportion of samples for which the genotype score is \"1\" ",
               "AvgReadDepth" : "The sum of the tag read counts for all samples, divided by the number of samples with non-zero tag read counts.",
               "AlleleSequence" : "The sequence of the tag which is present in samples with genotype score \"1\"",
               "TrimmedSequence" : "Same as the full sequence, but with removed adapters in short marker tags",
               "CloneID" : "Unique identifier of the sequence tag",
               "StDevReadDepth" : "The standard deviation of the number of tag reads for all samples with non-zero tag read counts"
            },
            "headerrowsnumber" : 7,
            "lastdatacol" : 1990,
            "notdescribedmetacolumns" : 0,
            "idcolposition" : 1,
            "firstdatacol" : 15,
            "alncoldetails" : {
               "Chrom_" : "Contig(s) with the best alignment of marker / tag to an existing model genome",
               "AlnEvalue_" : "E value of the best alignment to an existing model genome",
               "ChromPos_" : "Position(s) on contig(s) with the best alignment of marker / tag to an existing model genome",
               "AlnCnt_" : "Total count of aligning markers / tags with selection criteria described below"
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            "metacolspositions" : [
               2,
               3,
               4,
               5,
               6,
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               8,
               9,
               10,
               11,
               12,
               13,
               14
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               "4" : "well column position",
               "1" : "DArT plate barcode",
               "3" : "well row position",
               "0" : "Order number where sample belongs to - important for multi-orders reports",
               "2" : "client plate barcode",
               "5" : "sample comments"
            },
            "modelreferences" : {
               "Cassava_v61" : ""
            }
         },
         "description" : "SilicoDArT Format: SilicoDArTs are scored in a binary fashion, representing genetically \"dominant\" markers, with \"1\"=Presence and \"0\"=Absence of a restriction fragment with the marker sequence in genomic representation of the sample. \"-\" represents calls with non-zero counts, but too low counts to score confidently as \"1\" (often representing heterozygotes)",
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               ],
               "911118172005_G_7" : [
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               ],
               "911118172014_B_12" : [
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               ],
               "911118172021_B_6" : [
                  "911118172021",
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                  "B",
                  "6",
                  "BR.SET2.18.BR-18GS-076.8.3",
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                  "972697",
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                  "3517"
               ],
               "911118172008_F_8" : [
                  "911118172008",
                  "BR-18-CNPMF.Plate04",
                  "F",
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                  "BR.SET1.18.BR-18GS-037.3.362",
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                  "3517"
               ],
               "911118172021_G_11" : [
                  "911118172021",
                  "BR-18-CNPMF.Plate17",
                  "G",
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                  "BR.SET2.18.BR-18GS-001.9.16",
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                  "3517"
               ],
               "911118172010_B_4" : [
                  "911118172010",
                  "BR-18-CNPMF.Plate06",
                  "B",
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                  "3517"
               ]
            },
            "outsideordersamples" : {},
            "multigenotypesamples" : {
               "BR.SET1.18.BR-18GS-063.16.303" : [
                  [
                     "DCas18-3587",
                     "BR-18-CNPMF.Plate03",
                     "B",
                     "3"
                  ],
                  [
                     "DCas18-3587",
                     "BR-18-CNPMF.Plate04",
                     "A",
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                  ]
               ],
               "BR.SET1.18.BR-18GS-107.3.464" : [
                  [
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                     "D",
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                  ],
                  [
                     "DCas18-3587",
                     "BR-18-CNPMF.Plate06",
                     "C",
                     "7"
                  ]
               ],
               "BR.SET1.18.BR-18GS-094.52.424" : [
                  [
                     "DCas18-3587",
                     "BR-18-CNPMF.Plate03",
                     "C",
                     "12"
                  ],
                  [
                     "DCas18-3587",
                     "BR-18-CNPMF.Plate05",
                     "D",
                     "7"
                  ]
               ]
            }
         }
      }
   },
   "company" : {
      "webpage" : "http://www.diversityarrays.com/",
      "namefull" : "Diversity Arrays Technology Pty Ltd",
      "address" : "Building 3, Level D, University of Canberra\nBruce, ACT 2617, Australia"
   },
   "blast" : {
      "evalue" : "5e-3",
      "modelrefs" : [
         "Cassava_v61"
      ],
      "pctidentity" : "70"
   }
}