{"text_format":"3","workbook":"xlsx","n_sheets":1,"sheets":["Supplementary_table_1"],"not_rendered":{"defined_names":1},"read":"whole","date_system":"1900"}

{"sheet":"Supplementary_table_1","index":0,"n_rows":26,"n_cols":23,"rows_kept":26,"merged":[[5,7,5,14],[5,15,5,22]]}
["Within-host microevolution of eight time-serial isolates from a patient with multidrug-resistant tuberculosis and inadequate compliance to treatment"]
["Supplementary Table 1"]
["Analysis criteria: min depth 45 & SNP frequency 25% "]
["Excluded repetitive regions and SNPs with distance <20"]
["* the SNP doesn’t  meet the criteria buy we are confident of the quality of these call"]
[{"$nulls":7},"observed_variants",{"$nulls":7},"frequency (Number of reads of variant allele/total depth)"]
["Reference position",null,"variant_type","gene","nucleotid \nchange","aminoacid \nchange","Reference \ngenome","TB1","TB2","TB3","TB4","TB5","TB6","TB7","TB8","TB1","TB2","TB3","TB4","TB5","TB6","TB7","TB8"]
[319134,"unfixed","frameshift_variant","oplA|Rv0266c","2018_2019insG","Val674fs","ACC","ACC","ACC","ACC","ACCG","ACC","ACC","ACC","ACC",0,0,0,0.7,0,0,0,0]
[488149,"unfixed","missense_variant","pks6|Rv0405","2419G>T","Gly807Cys","G","G","G","G","G","G","T","G","G",0,0,0,0,0,"0.26 (24/94)",0,0]
[725989,"unfixed","missense_variant","recC|Rv0631c ","2318C>A","Ala773Asp","G","G","G","G","T","G","G","G","G",0,0,0,"0.3 (30/115)",0,0,0,0]
[880800,"fixed","conservative_inframe_deletion","Rv0785|Rv0785","1465_1482del","Ala489_Ile494del","GATCGCGGTCAAGCTGCACA","GATCGCGGTCAAGCTGCACA","GATCGCGGTCAAGCTGCACA","GA","GA","GA","GATCGCGGTCAAGCTGCACA","GA","GA",0,0,"1 (65/65)","1 (77/77)","1 (35/35)*",0,"1 (58/58)","1 (51/51)"]
[1144650,"fixed","synonymous_variant","eno|Rv1023","87C>T","Asp29Asp","C","C","C","C","C","C","C","T","T",0,0,0,0,0,0,"1 (48/48)","1 (58/58)"]
[1810164,"fixed","missense_variant","TB15.3|Rv1636","44A>C","Asp15Ala","G","G","G","G","G","G","G","A","A",0,0,0,0,0,0,"1 (78/78)","1 (51/51)"]
[1838646,"unfixed","synonymous_variant","uvrB|Rv1633","C1572T","Ala524Ala","C","C","C","C","C","C","C","C","T",0,0,0,0,0,0,0,"0.61 (90/148)"]
[2080907,"fixed","frameshift_variant","Rv1835c|Rv1835c","1678_1679insG","Pro561fs","GCC","GCC","GCC","GCC","GCC","GCC","GCC","GCC","GCC",0,0,0,0,0,0,"0.61 (39/64)","0.32 (14/44)*"]
[2401191,"fixed","missense_variant","Rv2141c|Rv2141c","532A>G","Thr178Ala","T","T","T","T","T","T","T","C","C",0,0,0,0,0,0,"1 (57/57)","1 (41/41)*"]
[2631962,"unfixed","synonymous_variant","plcA|Rv2351c","114A>C","Gly38Gly","A","A","A","A","C","A","A","C","A",0,0,0,"0.18 (33/184)*",0,0,"0.28 (27/95)",0]
[3014795,"fixed","missense_variant","Rv2699c|Rv2699c","171A>C","Glu57Asp","T","T","T","T","T","T","G","T","T",0,0,0,0,0,"130/161",0,0]
[3176130,"fixed","missense_variant","Rv2864c|Rv2864c","1136C>T","Thr379Ile","G","G","G","G","G","G","G","A","A",0,0,0,0,0,0,"1 (64/64)","1 (63/63)"]
[7570,"fixed","missense_variant","gyrA|Rv0006","269C>T","Ala90Val","C","C","C","C","C","C","T","C","C",0,0,0,0,0,"0.85 (77/91)",0,0]
[7581,"fixed","missense_variant","gyrA|Rv0006","280G>C","Asp94His","G","G","G","C","C","C","G","C","C",0,0,0.98,1,"0.99 (44/45)","<0.25 (11/90)","1 (59/59)","1 (70/70)"]
[8226,"fixed","missense_variant","gyrA|Rv0006","925C>T","Arg309Trp","C","C","C","C","C","C","C","C","T",0,0,0,0,0,0,0,"0.53 (39/73)"]
[779127,"unfixed","frameshift_variant","Rv0678|Rv0678 ","139dupG","Asp47fs","TGA","TGA","TGA","TGA","TGA","TGA","TGA","TGGA","TGGA",0,0,0,0,0,0,"0.8 (34/45)","0.39 (15/38)"]
[2288713,"fixed","frameshift_variant","pncA|Rv2043c","525_526insCG","Thr177fs","TGCG","TGCG","TGCG","TGCG","TGCG","TGCG","TGCG","TGCGCG","TGCGCG",0,0,0,0,0,0,"1 (46/47)","1 (17/17)*"]
[3568733,"fixed","intergenic_region","whiB7-uvrD2|Rv3197A-Rv3198c","3568733A>C",null,"A","A","A","A","A","A","A","C","C",0,0,0,0,0,0,"1 (90/90)","1 (56/56)"]
[4327211,"fixed","frameshift_variant","ethA|Rv3854c","261_262insT","Thr88fs","GTG","GTG","GTG","GTG","GTG","GTG","GTG","GTTG","GTTG",0,0,0,0,0,0,"1 (128/128)","0.91 (86/94)"]