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["Transcriptional responses of the bacterium Burkholderia terrae BS001 to the fungal host Lyophyllum sp. strain Karsten under soil-mimicking conditions","Microbial Ecology",{"$nulls":3},"Irshad Ul Haq* Francisco Dini-Andreote and Jan Dirk van Elsas \n*Corresponding author: Irshad Ul Haq, Microbial Ecology Group, Groningen Institute of Evolutionary Life Sciences (GELIFES), Nijenborgh 7, 9747 AG, University of Groningen, The Netherlands.\nE‒mail address: i.u.haq@rug.nl\n"]
[]
["Overview of sequencing reads for treatment B and B+F",{"$nulls":4},"Sum of reads (3 replicates) for both  B and B+F treatments"]
["T1A (replicate 1)",{"$nulls":4},"T1A"]
["Total read number",1764563,{"$nulls":3},"Total read number",5265013]
["Number of unmapped reads",314413,{"$nulls":3},"Number of unmapped reads",942988]
["Number of reads mapped at least once",1450150,{"$nulls":3},"Number of reads mapped at least once",4322025]
["Number of reads mapped on rRNA",1124288,{"$nulls":3},"Number of reads mapped on rRNA",3135365]
["Number of reliable reads",1450096,{"$nulls":3},"Number of reliable reads",4321852]
["Number of reads kept on B. terrae BS001 genome",1450095,{"$nulls":3},"Number of reads kept on B. terrae BS001 genome",4321851]
["Total reads mapped on genomic objects (except rRNA) into B. terrae BS001 genome",352505,{"$nulls":3},"Total reads mapped on genomic objects (except rRNA) into B. terrae BS001 genome",1279800]
[]
["T1A (replicate 2)",{"$nulls":4},"T1C"]
["Total read number",1677269,{"$nulls":3},"Total read number",5880178]
["Number of unmapped reads",265925,{"$nulls":3},"Number of unmapped reads",991026]
["Number of reads mapped at least once",1411344,{"$nulls":3},"Number of reads mapped at least once",4889152]
["Number of reads mapped on rRNA",932812,{"$nulls":3},"Number of reads mapped on rRNA",3619043]
["Number of reliable reads",1411290,{"$nulls":3},"Number of reliable reads",4888912]
["Number of reads kept on B. terrae BS001 genome",1411290,{"$nulls":3},"Number of reads kept on B. terrae BS001 genome",4888911]
["Total reads mapped on genomic objects (except rRNA) into B. terrae BS001 genome",521730,{"$nulls":3},"Total reads mapped on genomic objects (except rRNA) into B. terrae BS001 genome",1385841]
[]
["T1A (replicate 3)",{"$nulls":4},"T2A"]
["Total read number",1823181,{"$nulls":3},"Total read number",5166756]
["Number of unmapped reads",362650,{"$nulls":3},"Number of unmapped reads",1070636]
["Number of reads mapped at least once",1460531,{"$nulls":3},"Number of reads mapped at least once",4096120]
["Number of reads mapped on rRNA",1078265,{"$nulls":3},"Number of reads mapped on rRNA",3326253]
["Number of reliable reads",1460466,{"$nulls":3},"Number of reliable reads",4096021]
["Number of reads kept on B. terrae BS001 genome",1460466,{"$nulls":3},"Number of reads kept on B. terrae BS001 genome",4096021]
["Total reads mapped on genomic objects (except rRNA) into B. terrae BS001 genome",405565,{"$nulls":3},"Total reads mapped on genomic objects (except rRNA) into B. terrae BS001 genome",837655]
[]
["T1C (replicate 1)",{"$nulls":4},"T2C"]
["Total read number",2093313,{"$nulls":3},"Total read number",5176877]
["Number of unmapped reads",332701,{"$nulls":3},"Number of unmapped reads",1093442]
["Number of reads mapped at least once",1760612,{"$nulls":3},"Number of reads mapped at least once",4083435]
["Number of reads mapped on rRNA","1228126.5",{"$nulls":3},"Number of reads mapped on rRNA",3130349]
["Number of reliable reads",1760487,{"$nulls":3},"Number of reliable reads",4083310]
["Number of reads kept on B. terrae BS001 genome",1760486,{"$nulls":3},"Number of reads kept on B. terrae BS001 genome",4083310]
["Total reads mapped on genomic objects (except rRNA) into B. terrae BS001 genome",576929,{"$nulls":3},"Total reads mapped on genomic objects (except rRNA) into B. terrae BS001 genome",1027877]
[]
["T1C (replicate 2)",{"$nulls":4},"T3A"]
["Total read number",1881870,{"$nulls":3},"Total read number",5003679]
["Number of unmapped reads",296069,{"$nulls":3},"Number of unmapped reads",931011]
["Number of reads mapped at least once",1585801,{"$nulls":3},"Number of reads mapped at least once",4072668]
["Number of reads mapped on rRNA","1209440.5",{"$nulls":3},"Number of reads mapped on rRNA",3400111]
["Number of reliable reads",1585737,{"$nulls":3},"Number of reliable reads",4072603]
["Number of reads kept on B. terrae BS001 genome",1585737,{"$nulls":3},"Number of reads kept on B. terrae BS001 genome",4072603]
["Total reads mapped on genomic objects (except rRNA) into B. terrae BS001 genome",417127,{"$nulls":3},"Total reads mapped on genomic objects (except rRNA) into B. terrae BS001 genome",746313]
[]
["T1C ((replicate 3)",{"$nulls":4},"T3C"]
["Total read number",1904995,{"$nulls":3},"Total read number",5339423]
["Number of unmapped reads",362256,{"$nulls":3},"Number of unmapped reads",1146311]
["Number of reads mapped at least once",1542739,{"$nulls":3},"Number of reads mapped at least once",4193112]
["Number of reads mapped on rRNA","1181475.5",{"$nulls":3},"Number of reads mapped on rRNA",3557525]
["Number of reliable reads",1542688,{"$nulls":3},"Number of reliable reads",4193038]
["Number of reads kept on B. terrae BS001 genome",1542688,{"$nulls":3},"Number of reads kept on B. terrae BS001 genome",4193038]
["Total reads mapped on genomic objects (except rRNA) into B. terrae BS001 genome",391785,{"$nulls":3},"Total reads mapped on genomic objects (except rRNA) into B. terrae BS001 genome",694625]
[]
["T2A (replicate 1)"]
["Total read number",1719355]
["Number of unmapped reads",366190,{"$nulls":3},"Key:"]
["Number of reads mapped at least once",1353165,{"$nulls":3},"T1 = Day 3"]
["Number of reads mapped on rRNA",1088199,{"$nulls":3},"T2 = Day 5"]
["Number of reliable reads",1353133,{"$nulls":3},"T3 = Day 8"]
["Number of reads kept on B. terrae BS001 genome",1353133]
["Total reads mapped on genomic objects (except rRNA) into B. terrae BS001 genome",286319,{"$nulls":3},"A = Assay treatment; Bacteria + Fungus (B+F)"]
[{"$nulls":5},"C = Control treatment without fungus; only bacteria (B)"]
["T2A (replicate 2)"]
["Total read number",1525692]
["Number of unmapped reads",353466]
["Number of reads mapped at least once",1172226]
["Number of reads mapped on rRNA",917932]
["Number of reliable reads",1172194]
["Number of reads kept on B. terrae BS001 genome",1172194]
["Total reads mapped on genomic objects (except rRNA) into B. terrae BS001 genome",279092]
[]
["T2A (replicate 3)"]
["Total read number",1921709]
["Number of unmapped reads",350980]
["Number of reads mapped at least once",1570729]
["Number of reads mapped on rRNA",1320122]
["Number of reliable reads",1570694]
["Number of reads kept on B. terrae BS001 genome",1570694]
["Total reads mapped on genomic objects (except rRNA) into B. terrae BS001 genome",272244]
[]
["T2C (replicate 1)"]
["Total read number",1847989]
["Number of unmapped reads",454895]
["Number of reads mapped at least once",1393094]
["Number of reads mapped on rRNA",1039927]
["Number of reliable reads",1393049]
["Number of reads kept on B. terrae BS001 genome",1393049]
["Total reads mapped on genomic objects (except rRNA) into B. terrae BS001 genome",369521]
[]
["T2C (replicate 2)"]
["Total read number",1785623]
["Number of unmapped reads",328998]
["Number of reads mapped at least once",1456625]
["Number of reads mapped on rRNA",1140340]
["Number of reliable reads",1456580]
["Number of reads kept on B. terrae BS001 genome",1456580]
["Total reads mapped on genomic objects (except rRNA) into B. terrae BS001 genome",345539]
[]
["T2C (replicate 3)"]
["Total read number",1543265]
["Number of unmapped reads",309549]
["Number of reads mapped at least once",1233716]
["Number of reads mapped on rRNA",950082]
["Number of reliable reads",1233681]
["Number of reads kept on B. terrae BS001 genome",1233681]
["Total reads mapped on genomic objects (except rRNA) into B. terrae BS001 genome",312817]
[]
["T3A (replicate 1)"]
["Total read number",1620884]
["Number of unmapped reads",301956]
["Number of reads mapped at least once",1318928]
["Number of reads mapped on rRNA",1151298]
["Number of reliable reads",1318907]
["Number of reads kept on B. terrae BS001 genome",1318907]
["Total reads mapped on genomic objects (except rRNA) into B. terrae BS001 genome",185882]
[]
["T3A (replicate 2)"]
["Total read number",1888385]
["Number of unmapped reads",341983]
["Number of reads mapped at least once",1546402]
["Number of reads mapped on rRNA","1219425.5"]
["Number of reliable reads",1546371]
["Number of reads kept on B. terrae BS001 genome",1546371]
["Total reads mapped on genomic objects (except rRNA) into B. terrae BS001 genome",365630]
[]
["T3A (replicate 3)"]
["Total read number",1494410]
["Number of unmapped reads",287072]
["Number of reads mapped at least once",1207338]
["Number of reads mapped on rRNA",1029387]
["Number of reliable reads",1207325]
["Number of reads kept on B. terrae BS001 genome",1207325]
["Total reads mapped on genomic objects (except rRNA) into B. terrae BS001 genome",194801]
[]
["T3C (replicate 1)"]
["Total read number",1711420]
["Number of unmapped reads",455696]
["Number of reads mapped at least once",1255724]
["Number of reads mapped on rRNA",1083045]
["Number of reliable reads",1255691]
["Number of reads kept on B. terrae BS001 genome",1255691]
["Total reads mapped on genomic objects (except rRNA) into B. terrae BS001 genome",184504]
[]
["T3C (replicate 2)"]
["Total read number",1475659]
["Number of unmapped reads",313537]
["Number of reads mapped at least once",1162122]
["Number of reads mapped on rRNA","918586.5"]
["Number of reliable reads",1162101]
["Number of reads kept on B. terrae BS001 genome",1162101]
["Total reads mapped on genomic objects (except rRNA) into B. terrae BS001 genome",264420]
[]
["T3C (replicate 3)"]
["Total read number",2152344]
["Number of unmapped reads",377078]
["Number of reads mapped at least once",1775266]
["Number of reads mapped on rRNA",1555893]
["Number of reliable reads",1775246]
["Number of reads kept on B. terrae BS001 genome",1775246]
["Total reads mapped on genomic objects (except rRNA) into B. terrae BS001 genome",245701]