GENES 2867:::H37Ra..7H9.shake.replicate.1 2867:::H37Ra..Dubos.media.replicate.2 2885:::Strain.CDC1551..replicate.3 4062:::MTB.strain.1254.Ctrl.vs.2hr.Hypoxia.rep.1 4068:::H37Rv.delta.mprAB.mutant.vs..H37Rv.delta.mprAB.mutant.SDS.treated.rep.2 4068:::H37Rv.vs..H37Rv.delta.mprAB.mutant.rep.4 4107:::X20ug.mL.CPZvsDMSO..6h 4365:::H37Rv.diamide.1h.rep.1 4396:::Strain.27.cDNA.Cy5.vs.H37Rv.gDNA.Cy3.rep.1 4396:::Strain.32.cDNA.Cy5.vs.H37Rv.gDNA.Cy3.rep.1 4489:::MTB1254.WT.vs.Rv3662c.3665c.KO.in.7H9OADC.Exp2..OD1.1 4523:::H37Rv.sigB.null.mutant.control.vs.5mM.Diamide.for.60.min.rep.2 4575:::Extracted.Lung.Surfactant.30min.rep.3 4575:::Purified.Surfactant.Lipids.30min.rep.2 4583:::X0.2ug.ml.PA.824.vs.DMSO.6hrs.rep.1 4583:::X0.2ug.ml.PA.824.vs.DMSO.6hrs.rep.2 4583:::X0.4ug.ml.PA.824.vs.DMSO.6hrs.rep.3 4583:::X0.4ug.ml.PA.824.vs.DMSO.6hrs.rep.4 4615:::AA_10uM_2h_T0_01 4615:::AA_30uM_10.min_06 4615:::AA_30uM_1h_05 4615:::AA_30uM_1h_08 4615:::AA_30uM_24h_T0_01 4615:::AA_30uM_30min_03 4615:::AA_30uM_30min_04 4615:::AA_60uM_24h_01 4615:::Acetate.3mM.10m.07 4615:::CK_LA_2h.2 4615:::CK_OA_NA_0.05_2h 4615:::CK_OA_NA_2h.02 4615:::CK.AA.Na.2h 4615:::CK.for.AA.NA.24h 4615:::CK.for.AA.NA.2h.2 4615:::CK.for.MDG.4h.PA.NA 4615:::CK.for.MDG.OA.4h 4615:::CK.for.OA.4h.1 4615:::CK.for.OA.NA..2h 4615:::CK.for.OA.PA.Na.4h 4615:::CK.LA.2h.4 4615:::CK.MDG.2h.for.PA.NA 4615:::CK.MDG.2h.for.PA.NA.2 4615:::CK.MDG.AA.Na.2h 4615:::CK.OA_NA_2H 4615:::CK.PA.NA.101801.2 4615:::CK.PA.NA.2h.02..100901 4615:::CK.PA.NA.2h.3..101801 4615:::CK.PA.Na.4h.2 4615:::ETYA_10uM_1h_02 4615:::ETYA_10uM.AA_1h_02 4615:::Glucose_5mM_10min_01 4615:::L2A_30uM_1h_02 4615:::L2A_30uM_1h_04 4615:::L2A_30uM_1h_06 4615:::L2A_30uM_1h_07 4615:::L2A_30uM_1h_09 4615:::L2A_30uM_30min_02 4615:::L2A_30uM_30min_05 4615:::L2A_30uM_30Min_06 4615:::L2A_30uM_30min_07 4615:::MDA_1254.pMV261_02 4615:::MDA_1254.pMV261_03 4615:::MDA_1254.pMV261.3524_01 4615:::MDA_1254.pMV261.3524_04 4615:::MDG_1254.pMV261_01 4615:::MDG_1254.pMV261_02 4615:::MDG_1254.pMV261_03 4615:::MDG_1254.pMV261.3524_01 4615:::MDG_1254.pMV261.3524_02 4615:::MDG_1254.pMV261.3524_03 4615:::MDG_1254.pMV261.3524_04 4615:::MTB1254_Bottom_10D_01 4615:::MTB1254_Bottom_10D_02 4615:::MTB1254_Bottom_10D_03 4615:::MTB1254_Bottom_10D_04 4615:::MTB1254_Bottom_14D_01 4615:::MTB1254_Bottom_14D_02 4615:::MTB1254_Bottom_14D_03 4615:::MTB1254_Bottom_14D_04 4615:::MTB1254_Bottom_21D_02 4615:::MTB1254_Bottom_21D_03 4615:::MTB1254_Bottom_21D_04 4615:::MTB1254_INH_20MIN 4615:::MTB1254_Pellicle_10D_01 4615:::MTB1254_Pellicle_10D_02 4615:::MTB1254_Pellicle_10D_03 4615:::MTB1254_Pellicle_14D_03 4615:::MTB1254_Pellicle_21D_01 4615:::MTB1254_Pellicle_21D_02 4615:::MTB1254_Pellicle_42D_01 4615:::MTB1254_Pellicle_42D_02 4615:::MTB1254_Pellicle_42D_04 4615:::MTB1254.0485.1._OA_10m_02 4615:::MTB1254.0485.1._OA_30m_01 4615:::MTB1254.0485.1._PA_30m_01 4615:::MTB1254.3524.1._OA_10min_02 4615:::MTB1254.3524.1._OA_10min_03 4615:::MTB1254.3524.1._OA_10min_04 4615:::MTB1254.3524.1._PA_12h_01 4615:::MTB1254.3524.1._PA_12h_02 4615:::MTB1254.3524.1.T0_WtT0_01 4615:::MTB1254.B4.1._OA_30MIN_01 4615:::MTB1254.B4.1._OA_30MIN_02 4615:::MTB1254.B4.1._OA_30MIN_03 4615:::MTB1254.B4.1._OA_30MIN_04 4615:::MTB1254.B4.1._PA_10MIN_01 4615:::MTB1254.B4.1._PA_30MIN_01 4615:::MTB1254.B4.1._PA_30MIN_03 4615:::MTB1254.B4.1._PA_30MIN_04 4615:::MTB1254.B4.1.Compl._OA_30MIN_02 4615:::MTB1254.B4.1.Compl._OA_30MIN_03 4615:::MTB1254.B4.1.Compl._OA_30MIN_04 4615:::MTB1254.B4.1.Compl._PA_30MIN_02 4615:::MTB1254.B4.1.Compl._PA_30MIN_03 4615:::MTB1254.B4.1.Compl._PA_30MIN_04 4615:::MTB1254.fadA._01 4615:::MTB1254.Rv0465c.4._PA50.OA30_30m_01 4615:::MTB1254.Rv3524.2._PA50.OA30_2h_02 4615:::MTB1254.whiB4_SDS_90MIN_01 4615:::MTB1254TA1_OA.30min_01 4615:::MTB1254TA1_OA.30min_03 4615:::MTB1254TA1_OA.30min_04 4615:::MTB1370_PA50_1h_01 4615:::MTB1370_PA50_1h_03 4615:::OA_50uM_10min_06 4615:::OA_50uM_1h_02 4615:::OA_50uM_1h_04 4615:::OA_50uM_1h_05 4615:::OA_50uM_1h_06 4615:::OA_50uM_1h_09 4615:::OA_50uM_1h_10 4615:::OA_50uM_24h_04 4615:::OA_50uM_24h_06 4615:::OA_50uM_2h..1.0..BSA.10mMGlu._30.min._01 4615:::OA_50uM_30min_04 4615:::OA_50uM_30min_05 4615:::OA_50uM_30min_08 4615:::OA_50uM_4h_05 4615:::OA_50uM.0.5.BSA_1h_01 4615:::PA_100uM_2h_T0_01 4615:::PA_100uM_4h_T0_01 4615:::PA_10uM_2h_T0_01 4615:::PA_50uM_10min_09 4615:::PA_50uM_1h_04 4615:::PA_50uM_1h_07 4615:::PA_50uM_1h_08 4615:::PA_50uM_1h_09 4615:::PA_50uM_1h_10 4615:::PA_50uM_1h_12 4615:::PA_50uM_24h_T0 4615:::PA_50uM_2h_04 4615:::PA_50uM_2h_T0_01 4615:::PA_50uM_30.min_05 4615:::PA_50uM_30.min_06 4615:::PA_50uM_30min_01 4615:::PA_50uM_30min_02 4615:::PA_50uM_30min_03 4615:::PA_50uM_30min_08 4615:::PA_50uM_30min_10 4615:::PA_50uM_30min_11 4615:::PA_50uM_3d_01 4615:::PA_50uM_3d_03 4615:::PA_50uM_3d_04 4615:::PA_50uM_3d_05 4615:::PA_50uM_3d_06 4615:::PA_50uM.0.5.BSA_1h_01 4615:::PA_50uM.AA_30uM_30min_01 4615:::PA_50uM.AA_30uM_30min_03 4615:::PA_50uM.AA_30uM_30min_04 4615:::PA_50uM.MAPP_30m_01 4615:::PA_50uM.OA_10uM_24h_02 4615:::PA_50uM.OA_10uM_2h_01 4615:::PA_50uM.OA_10uM_2h_04 4615:::PA_50uM.OA_30uM_24h_02 4615:::PA_50uM.OA_30uM_2h_01 4615:::PA_50uM.OA_30uM_30min_03 4615:::PA_5uM_2h_T0_01 4615:::Rv_OA30_30mim_03 4615:::Rv_Rv3524.1_OA_10min 4615:::Rv_TA_OA30_30mim_03 4615:::Rv.MT106_100603_01 4615:::Rv.MT96_100503_01 4615:::Rv.MT96_100603_01 4615:::Rv.pMV0481.2. 4615:::Starvation_1254_12h_03 4615:::Starvation_1254_12h_04 4615:::Starvation_1254_24h_02 4615:::Starvation_1254_24h_04 4615:::Starvation_1254_24h_05 4615:::Starvation_1254_24h_06 4615:::Starvation_1254_24h_07 4615:::Starvation_1254_24h_08 4615:::Starvation_1254_3d_01 4615:::Starvation_1254_3d_04 4615:::Starvation_1254_5d_01 4615:::Starvation_1254_5d_02 4615:::Starvation_1254_5d_03 4615:::Starvation_1254_5d_04 4615:::Starvation_1254_6h_01 4615:::Starvation_1254_6h_05 4615:::Starvation_1254_6h_06 4615:::Starvation_1254_OA50_24h_02 4615:::Starvation_1254_OA50_3d_01 4615:::Starvation_1254_OA50_3d_02 4615:::Starvation_1254_OA50_3d_03 4615:::Starvation_1254_OA50_3d_04 4615:::Starvation_1254_OA50_5d_01 4615:::Starvation_1254_OA50_5d_02 4615:::Starvation_1254_OA50_5d_03 4615:::Starvation_1254_OA50_5d_04 4615:::Starvation_1254_PA50.OA30_6h_01 4615:::TBD094 4615:::TBD1115 4615:::TBD1267 4615:::TBD1275 4615:::TBD622 4615:::TBD625 4615:::TBD662 4615:::TBD663 4615:::TBE057 4615:::TBE058 4615:::TBE283 4615:::TBE733 4615:::TBE735 4615:::TBF466 4615:::Test_261B4.1 4615:::Test_361.1 4615:::Test_361.3 4615:::Test_ceramide_5uM 4615:::Test.1 4615:::Tet_50ng_30M_01 4615:::WM_1254_vs_1254whiB4_20day 4615:::WT_85.1_PA_10min_02 4615:::WT_WhiB4_OA_10min_01 4615:::X2.2..Dipyridyl_0.2mM.Dpd.AA_50uM_01 4615:::X7H9_MTB1254.3524.1._OA50_10M_01 4696:::H37Rv.wt.vs.dosS.null.anaerobic.Gaspak.24hr.rep.2 4699:::CDC1551.Ctrl.vs.clinical.isolate.1934.03_Beijing.rep.2 4703:::Clinical.isolate.2169.99_Uganda.extra.vs.intracellular.in.resting.macrophages.rep.2 4703:::Clinical.isolate.947.01_EAI.extra.vs.intracellular.in.resting.macrophages.rep.2 4815:::H37Rv.reaeration.for.1hrs.rep.5 RV0244C NA NA -1.69971671388102 0.207535618300491 0.271441403203996 NA -0.833194467588735 -0.128474430376494 -1.39113719142048 -0.674490759476595 NA -0.674490759476595 -0.237320822778802 -0.686981329096532 -1.00200790710706 -0.736102896159553 -0.956609490603825 -0.982551442891386 -0.680976247548486 2.2180369205865 0.466955141176104 -0.278875987091285 -0.726374664051718 1.02470711535867 1.12847492450892 -0.75880210441117 -0.661519783332815 -0.76528759248306 -0.661519783332815 -0.408585748529091 -0.609635878757692 -0.687461735620376 -0.557751974182569 -0.661519783332815 -0.57072295032635 -0.739345640195499 NA -0.894997353920867 -0.713403687907937 -0.817171497058183 -0.447498676960433 -0.95985223463977 -0.784744056698731 -0.726374664051718 -0.778258568626841 -0.642063319117144 -0.434527700816653 0.505868069607446 0.739345640195499 -0.603150390685801 0.460469653104214 0.428042212744762 0.473440629247995 0.745831128267389 -0.674490759476595 2.06238520686113 NA 0.76528759248306 0.57720843839824 -0.19456464215671 -0.447498676960433 0.0259419522875613 -0.168622689869149 -0.278875987091285 -0.220506594444272 -0.415071236600982 -0.473440629247995 -0.291846963235065 -0.395614772385311 -0.538295509966898 -0.233477570588052 -0.214021106372381 -0.304817939378846 -0.311303427450736 0.0778258568626841 0.784744056698731 -0.0907968330064648 0.239963058659943 -0.648548807189034 -0.557751974182569 -0.291846963235065 -0.57072295032635 -0.311303427450736 -0.136195249509697 -0.155651713725368 0.0648548807189034 -0.674490759476595 -0.557751974182569 -1.64082848218826 -0.940395770424099 -0.674490759476595 2.02995776650168 1.78999470784173 2.8211873112723 1.42032188774398 1.97158837385466 1.78350921976984 1.28412663823429 1.32952505473752 -0.609635878757692 1.8094511720574 NA 1.51760420882234 2.63959364525937 1.85484958856064 2.36720314623997 2.0169867903579 2.11426911143625 1.46572030424722 2.49042741960589 2.0169867903579 2.77578889476906 1.93267544542332 1.49814774460667 -1.21278626944349 2.77578889476906 1.8807915408482 -1.36195249509697 1.52408969689423 1.82890763627308 1.75756726748228 2.5487968122529 2.6849920617626 1.3424960308813 2.10129813529247 2.43205802695888 1.58894457761313 1.93267544542332 0.836627961273854 1.64082848218826 -0.531810021895008 -0.622606854901472 -0.823656985130073 2.05589971878924 2.25046436094595 1.36195249509697 0.162137201797258 0.674490759476595 1.61488652990069 2.06238520686113 -0.544780998038788 1.87430605277631 1.80296568398551 1.90673349313576 1.97158837385466 1.99104483807033 NA 2.65256462140315 0.207535618300491 1.32303956666563 1.8094511720574 1.98455934999844 2.32180472973674 NA 1.05064906764624 2.10778362336436 NA 2.13372557565192 1.52408969689423 -0.434527700816653 -0.38264379624153 -0.473440629247995 -0.479926117319885 -0.220506594444272 1.31655407859374 1.99753032614222 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0.00684762192362026 -0.855952740452532 NA -1.27365767779337 -1.77353407821765 -0.924428959688735 -0.999752800848557 -1.41061011626577 -1.21887670240441 -1.42430536011301 -1.08877188585562 -0.376619205799114 0.643676460820304 0.349228718104633 -0.746390789674608 0.657371704667545 1.39006725049491 0.595743107354962 0.540962131966 0 1.80092456591213 1.08877188585562 1.37637200664767 1.36952438472405 -0.588895485431342 -0.705305058132886 -0.629981216973064 -1.02029566661942 -0.294447742715671 -0.568352619660481 -0.629981216973064 -0.390314449646355 -0.417704937340836 -0.493028778500658 -0.362923961951874 -0.554657375813241 -0.499876400424279 -0.520419266195139 -0.671066948514785 -0.965514691230456 -0.753238411598228 -0.719000301980127 -0.602590729278583 -0.513571644271519 -0.520419266195139 -0.397162071569975 -0.410857315417215 -0.992905178924937 -0.890190850070633 -0.616285973125823 -0.951819447383216 -0.760086033521848 -1.10931475162648 -1.67766737128696 -1.20518145855717 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POSITION A C G T 1 0 0 0.555556 0.444444 2 0.777778 0.111111 0.111111 0 3 0.555556 0.222222 0.222222 0 4 0.222222 0.666667 0 0.111111 5 0 0.333333 0 0.666667 6 0.555556 0 0.222222 0.222222 7 0.222222 0 0 0.777778 8 0.111111 0 0.555556 0.333333 9 0.111111 0.777778 0.111111 0 10 0.444444 0 0.333333 0.222222 11 0.555556 0 0.444444 0 12 0.666667 0.222222 0.111111 0 13 0.666667 0.111111 0.222222 0 14 0 0 1 0 15 0.222222 0 0.777778 0 16 0.777778 0 0 0.222222 17 0.111111 0 0 0.888889 18 0 0.111111 0.111111 0.777778 19 0.333333 0.666667 0 0 20 0.444444 0.222222 0 0.333333 21 0.111111 0.666667 0 0.222222

POSITION A C G T 1 0.727273 0.181818 0.090909 0 2 0.909091 0.090909 0 0 3 0 0 0.727273 0.272727 4 0 0 0 1 5 0 0 0 1 6 0 0 1 0 7 0.363636 0 0 0.636364