{ "orders" : { "DCas19-4078" : { "clientemail" : "kawukisezirobert@gmail.com", "orderdatetime" : "2019-02-12 01:57:20", "clientname" : "Dr. Robert Kawuki", "productname" : "Cassava DArTseq (1.0)" } }, "errormsg" : "OK", "error" : 0, "datafiles" : { "Report_DCas19-4078_SilicoDArT_1.csv" : { "filetype" : "SilicoDArT", "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", "CallRate" : "The proportion of samples for which the genotype call is either \"1\" or \"0\", rather than \"-\" ", "OneRatio" : "The proportion of samples for which the genotype score is \"1\" ", "AvgReadDepth" : "The sum of the tag read counts for all samples, 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"DCas19-4078", "1", "A", "3" ], [ "DCas19-4078", "1", "E", "3" ] ], "CycleOne_Clonal_NaCRRI2016_244" : [ [ "DCas19-4078", "2", "B", "10" ], [ "DCas19-4078", "2", "B", "4" ] ] } } }, "Report_DCas19-4078_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", "CloneID" : "Unique identifier for the sequence in which the SNP marker occurs", "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" : 225, "notdescribedmetacolumns" : 0, "idcolposition" : 1, "firstdatacol" : 23, "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", "22" ], "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_v7Phyto" : "" } }, "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)", "exportsnp" : [ { "filename" : "Report_DCas19-4078_SNP_mapping_2.csv", "type" : "mapping", "description" : "SNP 1 Row Mapping Format: \"0\" = Reference allele homozygote, \"1\" = SNP allele homozygote, \"2\"= heterozygote and \"-\" = double null/null allele homozygote (absence of fragment with SNP in genomic representation)" } ], "sampleheaders" : { "notreportedsamples" : {}, "headers" : { "911119044011_D_4" : [ "911119044011", "2", "D", "4", "CycleOne_Clonal_NaCRRI2016_343", "Cassava", "1151349", "none", "4008" ], "911119044010_C_10" : [ "911119044010", "1", "C", "10", "CycleTwo_Parent_66", "Cassava", "1151302", "none", "4008" ], "911119044010_G_7" : [ "911119044010", "1", "G", "7", "CycleTwo_Parent_15", "Cassava", "1151282", "none", "4008" ], "911119044011_A_2" : [ "911119044011", "2", "A", "2", "CycleTwo_Parent_39", "Cassava", "1151330", "none", "4008" ], "911119044011_F_4" : [ "911119044011", "2", 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