{"text_format":"2","workbook":"xlsx","n_sheets":2,"sheets":["Short_reads_raw_and_trimmedData","Long_reads_PacBio_Iso-Seq"],"not_rendered":{"charts":0,"images":0,"macros":0,"external_links":0,"defined_names":0,"comments":1,"pivot_tables":0},"unopened":[],"bounds":{"document_bytes":16777216,"sheet_cells":100000,"run_cost":"one","rows_first":2000,"rows_last":500,"rows_between":2000,"halvings":0,"cell_chars":16384,"cell_head_chars":4096},"cells_cut":0,"cells_raw":0,"read":"whole","date_system":"1900"}

{"sheet":"Short_reads_raw_and_trimmedData","index":0,"n_rows":73,"n_cols":18,"rows_kept":73,"cut":false,"hidden":false,"merged":[[1,0,1,6],[2,0,2,6]]}
["# Illumina and Solid raw reads pre-processing"]
["# CLC Genomics Workbench 6-10"]
["# parameters used for trimming\n# Removal of low quality sequences (limit = 0.05). \n# Removal of ambiguous nucleotides: No ambiguous nucleotides allowed. \n# Removal of adapter sequences and polyA. \n# Removal of sequences on length: minimum length 16 nucleotides and maximum length 1,000 nucleotides."]
["Cultivar","SampleID","Number of reads","Avg.length","Number of reads after trim","Percentage trimmed","Avg.length after trim","Sequencing technology","Library type","SRA ID","Tissue","Inoculation/infestation/treatment","Days post inoculation/infestation/treatment","Plants growth conditions","Vectors or transgenic elements present ","Orientation of reads in pair","Read strandness","Data Source"]
["Desiree","Desiree_PVY_l1_1",53899470,90,53899470,{"$f":"E5/C5","v":1},89.9,"Illumina","DSN PE90 unstranded","SRR10070125","leaf","PVY","na","growth chamber","na","fr","both","NIB"]
["Desiree","CONT_coi1",49158746,90,49158746,{"$f":"E6/C6","v":1},90,"Illumina","PE90 unstranded","SRR1207288","leaf","control",1,"growth chamber","coi1-RNAi element","fr","both","NIB"]
["Desiree","CONT_NT",48679626,90,48679626,1,90,"Illumina","PE90 unstranded","SRR1207290","leaf","control",1,"growth chamber","na","fr","both","NIB"]
["Desiree","CPB_coi1",47988790,90,47988790,1,90,"Illumina","PE90 unstranded","SRR1207287","leaf","CPB",1,"growth chamber","coi1-RNAi element","fr","both","NIB"]
["Desiree","CPB_NT",49224502,90,49224502,1,90,"Illumina","PE90 unstranded","SRR1207289","leaf","CPB",1,"growth chamber","na","fr","both","NIB"]
["Desiree","SRR3161991",11642703,49,11596396,0.99602265899937492,47.3,"Illumina","SE50 unstranded","SRR3161991","leaf","control","na","field","na","na","both","ENA"]
["Desiree","SRR3161995",11742842,49,11713708,0.99751899923374598,48,"Illumina","SE50 unstranded","SRR3161995","leaf","drought","na","field","na","na","both","ENA"]
["Desiree","SRR3161999",11835090,49,11787063,0.99594198269721645,47.2,"Illumina","SE50 unstranded","SRR3161999","leaf","control","na","greenhouse","na","na","both","ENA"]
["Desiree","SRR3162003",12066501,49,12023318,0.99642124920886344,47.5,"Illumina","SE50 unstranded","SRR3162003","leaf","drought","na","greenhouse","na","na","both","ENA"]
["Desiree","SRR3162007",12412385,49,12368684,0.99647924230516538,47.5,"Illumina","SE50 unstranded","SRR3162007","leaf","control","na","greenhouse","na","na","both","ENA"]
["Desiree","SRR3162011",11869495,49,11840459,0.99755372911821438,48,"Illumina","SE50 unstranded","SRR3162011","leaf","drought","na","greenhouse","na","na","both","ENA"]
["Desiree","SRR3162015",12319733,49,12286870,0.99733249089083342,47.9,"Illumina","SE50 unstranded","SRR3162015","leaf","control","na","greenhouse","na","na","both","ENA"]
["Desiree","SRR3162019",11823475,49,11795018,0.9975931779785554,48,"Illumina","SE50 unstranded","SRR3162019","leaf","drought","na","greenhouse","na","na","both","ENA"]
["Desiree","SRR3162023",18275400,49,18229735,0.99750128588156761,47.8,"Illumina","SE50 unstranded","SRR3162023","leaf","control","na","field","na","na","both","ENA"]
["Desiree","SRR3162027",19163175,49,19116224,0.99754993627099897,47.9,"Illumina","SE50 unstranded","SRR3162027","leaf","drought","na","field","na","na","both","ENA"]
["Desiree","SRR3162031",20086368,49,20015876,0.99649055518648266,47.5,"Illumina","SE50 unstranded","SRR3162031","leaf","control","na","field","na","na","both","ENA"]
["Desiree","SRR3162035",19487715,49,19422314,0.99664398827671685,47.5,"Illumina","SE50 unstranded","SRR3162035","leaf","drought","na","field","na","na","both","ENA"]
["Desiree","SRR4125238",10635534,101,10549062,0.99186951966868797,95.1,"Illumina","SE100 unstranded","SRR4125238","seedlings","na","na","na","na","na","both","ENA"]
["Desiree","SRR4125239",8283180,101,8220010,0.99237370188743934,95.1,"Illumina","SE100 unstranded","SRR4125239","seedlings","na","na","na","na","na","both","ENA"]
["Desiree","SRR4125240",8043687,101,7977558,0.99177877010878224,94.8,"Illumina","SE100 unstranded","SRR4125240","seedlings","na","na","na","na","na","both","ENA"]
["Desiree","SRR4125241",7944852,101,7878199,0.99161054227316003,94.4,"Illumina","SE100 unstranded","SRR4125241","seedlings","na","na","na","na","na","both","ENA"]
["Desiree","SRR4125242",6271920,101,6123998,0.97641519662240595,86.8,"Illumina","SE100 unstranded","SRR4125242","seedlings","na","na","na","na","na","both","ENA"]
["Desiree","SRR4125243",9980929,101,9536006,0.95542268660562557,84.4,"Illumina","SE100 unstranded","SRR4125243","seedlings","na","na","na","na","na","both","ENA"]
["Desiree","SRR4125244",9661094,101,9534596,0.98690645179521075,93.4,"Illumina","SE100 unstranded","SRR4125244","seedlings","na","na","na","na","na","both","ENA"]
["Desiree","SRR4125245",10087171,101,9997955,0.99115549840485506,95.2,"Illumina","SE100 unstranded","SRR4125245","seedlings","na","na","na","na","na","both","ENA"]
["Desiree","SRR4125246",9248282,101,9140995,0.98839925080139213,94.5,"Illumina","SE100 unstranded","SRR4125246","seedlings","na","na","na","na","na","both","ENA"]
["Desiree","SRR4125247",4256250,101,4249828,0.99849116005873717,98.2,"Illumina","SE100 unstranded","SRR4125247","seedlings","na","na","na","na","na","both","ENA"]
["Desiree","SRR4125248",5972182,101,5942451,0.99502175251859371,98.1,"Illumina","SE100 unstranded","SRR4125248","root","na","na","na","na","na","both","ENA"]
["Desiree","SRR4125249",5193719,101,5176844,0.99675088313403171,98.1,"Illumina","SE100 unstranded","SRR4125249","root","na","na","na","na","na","both","ENA"]
["Desiree","SRR4125250",6644676,101,6617306,0.99588091277889246,97.8,"Illumina","SE100 unstranded","SRR4125250","root","na","na","na","na","na","both","ENA"]
["Desiree","SRR4125251",5219511,101,5207958,0.99778657425954276,98.1,"Illumina","SE100 unstranded","SRR4125251","root","na","na","na","na","na","both","ENA"]
["Desiree","SRR4125252",3881450,101,3871776,0.99750763245694263,98,"Illumina","SE100 unstranded","SRR4125252","root","na","na","na","na","na","both","ENA"]
["Desiree","ERR305632_1(paired)",52870782,89.2,52476427,0.9925411543941226,86.1,"Illumina","PE90 unstranded","ERR305632","leaf","Phytophthora_infestans",1,"na","na","fr","both","ENA"]
["Desiree","ERR305632_1(orphans)",1575,78,1459,0.92634920634920637,51.6,"Illumina","PE90 unstranded","ERR305632","leaf","Phytophthora_infestans",1,"na","na","fr","both","ENA"]
["Desiree","17_4_cut",7515886,48.9,5042977,0.67097571730066152,39.200000000000003,"SOLiD","SE50 unstranded","SRR10065428, SRR10065429","leaf","mock",3,"growth chamber","na","na","both","NIB"]
["Desiree","17_2_cut",9885885,49.3,7265120,0.73489829185753219,36.9,"SOLiD","SE50 unstranded","SRR10065428, SRR10065429","leaf","mock",3,"growth chamber","na","na","both","NIB"]
["Desiree","17_3_cut",20884043,48.9,12069307,0.57792004163178556,35.9,"SOLiD","SE50 unstranded","SRR10065428, SRR10065429","leaf","mock",3,"growth chamber","na","na","both","NIB"]
["Desiree","17_1_cut",8959293,49.2,6973672,0.77837302563941146,37.6,"SOLiD","SE50 unstranded","SRR10065428, SRR10065429","leaf","mock",3,"growth chamber","na","na","both","NIB"]
["Desiree","18_1_cut",6442198,48.8,5014109,0.77832270911263512,36.9,"SOLiD","SE50 unstranded","SRR10065428, SRR10065429","leaf","PVY",3,"growth chamber","na","na","both","NIB"]
["Desiree","18_2_cut",7063576,48.8,5201348,0.73636186543473159,36.299999999999997,"SOLiD","SE50 unstranded","SRR10065428, SRR10065429","leaf","PVY",3,"growth chamber","na","na","both","NIB"]
["Desiree","18_3_cut",37397073,48.6,21342318,0.57069487764456861,35.6,"SOLiD","SE50 unstranded","SRR10065428, SRR10065429","leaf","PVY",3,"growth chamber","na","na","both","NIB"]
["Desiree","22_1_cut",10701303,48.8,7999325,0.74750943880385412,36.200000000000003,"SOLiD","SE50 unstranded","SRR10065428, SRR10065429","stem","na","na","growth chamber","na","na","both","NIB"]
["Desiree","22_2_cut",45128099,48.5,26108317,0.57853793043664437,35.200000000000003,"SOLiD","SE50 unstranded","SRR10065428, SRR10065429","stem","na","na","growth chamber","na","na","both","NIB"]
["PW363","PW363Ry-_l1",52609184,90,52609184,1,89.9,"Illumina","DSN PE90 unstranded","SRR10070123, SRR10070123","leaf","PVY",3,"growth chamber","na","fr","both","NIB"]
["PW365","PW363Ry+_l1",51732846,90,51732846,1,89.9,"Illumina","DSN PE90 unstranded","SRR10070123, SRR10070123","leaf","PVY",3,"growth chamber","na","fr","both","NIB"]
["PW363","13_1_cut",7403065,49.6,5684770,0.76790000000000003,37.700000000000003,"SOLiD","SE50 unstranded","SRR10065430 - SRR10065433","leaf","mock",3,"growth chamber","na","na","both","NIB"]
["PW363","13_2_cut",8302545,49.7,5878593,0.70799999999999996,36.9,"SOLiD","SE50 unstranded","SRR10065430 - SRR10065433","leaf","mock",3,"growth chamber","na","na","both","NIB"]
["PW363","13_3_cut",19679423,49.6,10220080,0.51929999999999998,35.1,"SOLiD","SE50 unstranded","SRR10065430 - SRR10065433","leaf","mock",3,"growth chamber","na","na","both","NIB"]
["PW363","14_1_cut",6583304,49.5,5270166,0.80049999999999999,37.700000000000003,"SOLiD","SE50 unstranded","SRR10065430 - SRR10065433","leaf","PVY",3,"growth chamber","na","na","both","NIB"]
["PW363","14_2_cut",7159218,49.6,5495364,0.76759999999999995,37.1,"SOLiD","SE50 unstranded","SRR10065430 - SRR10065433","leaf","PVY",3,"growth chamber","na","na","both","NIB"]
["PW363","14_3_cut",34957041,49.4,21283089,0.60880000000000001,35.9,"SOLiD","SE50 unstranded","SRR10065430 - SRR10065433","leaf","PVY",3,"growth chamber","na","na","both","NIB"]
["PW363","15_1_cut",4861705,48.7,3097549,0.6371,37.299999999999997,"SOLiD","SE50 unstranded","SRR10065430 - SRR10065433","leaf","mock",3,"growth chamber","na","na","both","NIB"]
["PW363","15_2_cut",5953336,48.9,3219276,0.54079999999999995,36.6,"SOLiD","SE50 unstranded","SRR10065430 - SRR10065433","leaf","mock",3,"growth chamber","na","na","both","NIB"]
["PW363","15_3_cut",44272685,48.1,26434203,0.59709999999999996,35.200000000000003,"SOLiD","SE50 unstranded","SRR10065430 - SRR10065433","leaf","mock",3,"growth chamber","na","na","both","NIB"]
["PW363","16_1_cut",7142875,49.6,5438028,0.76129999999999998,37.4,"SOLiD","SE50 unstranded","SRR10065430 - SRR10065433","leaf","PVY",3,"growth chamber","na","na","both","NIB"]
["PW363","16_2_cut",29588327,49.6,17198202,0.58120000000000005,36.1,"SOLiD","SE50 unstranded","SRR10065430 - SRR10065433","leaf","PVY",3,"growth chamber","na","na","both","NIB"]
["PW363","16_3_cut",3760155,49.3,2267251,0.60299999999999998,38.6,"SOLiD","SE50 unstranded","SRR10065430 - SRR10065433","leaf","PVY",3,"growth chamber","na","na","both","NIB"]
["Rywal","SH086_S1",70623184,100.6,69150583,0.97909999999999997,98.4,"Illumina","PE100 strand-specific","SRX6801457 - SRX6801468","leaf","mock",3,"growth chamber","NahG transgene","fr","reverse","NIB"]
["Rywal","SH087_S2",59762572,100.6,58848024,0.98470000000000002,98.8,"Illumina","PE100 strand-specific","SRX6801457 - SRX6801468","leaf","mock",3,"growth chamber","NahG transgene","fr","reverse","NIB"]
["Rywal","SH088_S3",60927912,100.6,60203744,0.98809999999999998,99.1,"Illumina","PE100 strand-specific","SRX6801457 - SRX6801468","leaf","mock",3,"growth chamber","NahG transgene","fr","reverse","NIB"]
["Rywal","SH089_S4",47025982,100.6,46333721,0.98529999999999995,98.9,"Illumina","PE100 strand-specific","SRX6801457 - SRX6801468","leaf","PVY",3,"growth chamber","NahG transgene","fr","reverse","NIB"]
["Rywal","SH090_S5",53828334,100.6,52714208,0.97929999999999995,98.6,"Illumina","PE100 strand-specific","SRX6801457 - SRX6801468","leaf","PVY",3,"growth chamber","NahG transgene","fr","reverse","NIB"]
["Rywal","SH091_S6",66562628,100.6,65276650,0.98070000000000002,98.5,"Illumina","PE100 strand-specific","SRX6801457 - SRX6801468","leaf","PVY",3,"growth chamber","NahG transgene","fr","reverse","NIB"]
["Rywal","SH098_S7",63936006,100.6,62702382,0.98070000000000002,98.5,"Illumina","PE100 strand-specific","SRX6801457 - SRX6801468","leaf","mock",3,"growth chamber","NahG transgene; Pti5 silencing hairpin","fr","reverse","NIB"]
["Rywal","SH099_S8",52719800,100.6,51787800,0.98229999999999995,97.7,"Illumina","PE100 strand-specific","SRX6801457 - SRX6801468","leaf","mock",3,"growth chamber","NahG transgene; Pti5 silencing hairpin","fr","reverse","NIB"]
["Rywal","SH100_S9",54565282,100.6,53772059,0.98550000000000004,98.9,"Illumina","PE100 strand-specific","SRX6801457 - SRX6801468","leaf","mock",3,"growth chamber","NahG transgene; Pti5 silencing hairpin","fr","reverse","NIB"]
["Rywal","SH101_S10",60884296,100.6,60074998,0.98670000000000002,99,"Illumina","PE100 strand-specific","SRX6801457 - SRX6801468","leaf","PVY",3,"growth chamber","NahG transgene; Pti5 silencing hairpin","fr","reverse","NIB"]
["Rywal","SH102_S11",61619136,100.6,60584841,0.98319999999999996,98.7,"Illumina","PE100 strand-specific","SRX6801457 - SRX6801468","leaf","PVY",3,"growth chamber","NahG transgene; Pti5 silencing hairpin","fr","reverse","NIB"]
["Rywal","SH103_S12",57780944,100.6,56323961,0.9748,98,"Illumina","PE100 strand-specific","SRX6801457 - SRX6801468","leaf","PVY",3,"growth chamber","NahG transgene; Pti5 silencing hairpin","fr","reverse","NIB"]

{"sheet":"Long_reads_PacBio_Iso-Seq","index":1,"n_rows":5,"n_cols":15,"rows_kept":5,"cut":false,"hidden":false,"merged":[]}
["# PacBio Iso-Seq dataset"]
["# processed using Iso-Seq 3 and Cupcake ToFU"]
["Cultivar","SampleID","Number of reads","Avg.length","Sequencing technology","Library type","SRA_ID","Tissue","Inoculation/infestation/treatment","Days post inoculation/infestation/treatment","Plants growth conditions","Vectors or transgenic elements present ","Sequencing read length","Read strandness","Data Source"]
["Rywal","Rywal_IsoSeq_S1",28209,2164,"PacBio","Iso-Seq","SRR8281993 - SRR8282000","leaf","mock",3,"growth chamber","na","full-length transcripts","forward","NIB"]
["Rywal","Rywal_IsoSeq_S2",28576,2172,"PacBio","Iso-Seq","SRR8282001 - SRR8282008","leaf","PVY",3,"growth chamber","na","full-length transcripts","forward","NIB"]