breseq  version 0.35.4  revision f352f80f4bc9
mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Marginal read alignment evidence (highest frequency 20 of 25 shown, sorted by frequency from high to low)
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_002947_CJ‑RC5,684,2304.G100.0% 10.4 / NA 5intergenic (‑133/+71)PP_4986/PP_4987hemolysin III family channel protein/putative Chemotaxis protein
*NC_002947_CJ‑RC1,070,2461.G57.7% 36.2 / 37.1 27intergenic (+46/+96)aroP‑I/PP_0928aromatic amino acid transport protein/K+‑dependent Na+/Ca+ exchanger‑like protein
*NC_002947_CJ‑RC170,8330AG57.1% ‑6.5 / 11.2 16intergenic (+14/‑556)PP_0159/PP_16SAfamily III CoA‑transferase/16S ribosomal RNA
*NC_002947_CJ‑RC1,070,2462.A55.6% 33.0 / 41.9 27intergenic (+46/+96)aroP‑I/PP_0928aromatic amino acid transport protein/K+‑dependent Na+/Ca+ exchanger‑like protein
*NC_002947_CJ‑RC1,327,1210CT53.6% 26.8 / 153.8 110intergenic (+97/‑196)PP_16SE/PP_23SE16S ribosomal RNA/23S ribosomal RNA
*NC_002947_CJ‑RC4,348,8120AG48.2% 39.0 / 161.0 111intergenic (‑70/+404)PP_3820/galUgroup II intron‑encoding maturase/UTP‑glucose‑1‑phosphate uridylyltransferase
*NC_002947_CJ‑RC4,158,4710AC44.8% 8.9 / 12.8 31S161R (AGC→CGC) PP_3661membrane protein
*NC_002947_CJ‑RC5,174,9380GC43.8% 32.4 / 14.2 32intergenic (‑276/+56)fadD‑I/fadD‑IIlong‑chain‑fatty acid‑‑CoA ligase/long‑chain‑fatty acid‑‑CoA ligase
*NC_002947_CJ‑RC5,512,7110AC42.9% 24.8 / 13.8 43Q32P (CAG→CCG) urtBurea ABC transporter permease
*NC_002947_CJ‑RC699,7220AG40.5% 69.7 / 132.6 116intergenic (+115/‑129)PP_t06/PP_23SDtRNA‑Ala/23S ribosomal RNA
*NC_002947_CJ‑RC2,863,8290TG34.2% 21.1 / 11.1 39S297A (TCG→GCG) gllRHTH‑type transcriptional regulator GalR
*NC_002947_CJ‑RC3,989,3610AC32.2% 102.9 / 16.4 59T627P (ACC→CCC) oplA5‑oxoprolinase A
*NC_002947_CJ‑RC4,044,5690AC31.5% 88.3 / 11.1 54V380G (GTG→GGG) PP_3566MFS transporter
*NC_002947_CJ‑RC5,694,7940AC30.0% 132.0 / 16.8 80P118P (CCA→CCCPP_4994hypothetical protein
*NC_002947_CJ‑RC1,544,3590CG28.6% 47.2 / 12.3 28A388G (GCG→GGG) mdfAmultidrug MFS transporter
*NC_002947_CJ‑RC4,942,5640GT28.4% 195.5 / 13.7 81V105L (GTA→TTA) PP_4348cystathionine beta‑lyase
*NC_002947_CJ‑RC1,404,0250AC27.6% 122.5 / 12.3 58F553V (TTC→GTC) PP_1228methyl‑accepting chemotaxis transducer
*NC_002947_CJ‑RC3,660,7000CG25.4% 137.8 / 13.3 63C12S (TGC→TCC) PP_3224class II aldolase/adducin domain‑containing protein
*NC_002947_CJ‑RC4,433,5800GC25.0% 111.5 / 10.1 56intergenic (‑29/‑89)PP_5648/PP_3928hypothetical protein/hypothetical protein
*NC_002947_CJ‑RC251,2490AC24.1% 119.8 / 12.3 58intergenic (‑47/‑19)nfeD/PP_0201membrane bound peptidase NefD/hypothetical protein

Marginal new junction evidence (lowest skew 10 of 25 shown)
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NC_002947_CJ‑RC 4809877 =5 (0.070)22 (0.420) 15/222 3.6 64.9% intergenic (‑283/‑272) PP_4234/dsbD‑II bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2
?NC_002947_CJ‑RC = 5991750 20 (0.380)intergenic (+229/‑317) kefB‑III/PP_mr64 glutathione‑regulated potassium/H+ antiporter/C4 ncRNA
* ? NC_002947_CJ‑RC = 599158663 (0.910)20 (0.300) 18/276 4.0 29.7% intergenic (+65/‑481) kefB‑III/PP_mr64 glutathione‑regulated potassium/H+ antiporter/C4 ncRNA
?NC_002947_CJ‑RC 5991778 = 35 (0.530)intergenic (+257/‑289) kefB‑III/PP_mr64 glutathione‑regulated potassium/H+ antiporter/C4 ncRNA
* ? NC_002947_CJ‑RC = 55584232 (0.030)16 (0.230)
+GCC
14/286 5.3 89.1% intergenic (‑84/+87) PP_4887/PP_4888 hypothetical protein/methyl‑accepting chemotaxis transducer
?NC_002947_CJ‑RC 5558424 = 2 (0.030)intergenic (‑85/+86) PP_4887/PP_4888 hypothetical protein/methyl‑accepting chemotaxis transducer
* ? NC_002947_CJ‑RC = 295708034 (0.490)11 (0.160) 11/282 6.2 25.3% intergenic (+35/‑161) PP_2588/PP_2589 class III aminotransferase/aldehyde dehydrogenase family protein
?NC_002947_CJ‑RC 2957165 = 32 (0.480)intergenic (+120/‑76) PP_2588/PP_2589 class III aminotransferase/aldehyde dehydrogenase family protein
* ? NC_002947_CJ‑RC = 48098824 (0.060)13 (0.200) 10/268 6.3 29.3% intergenic (‑288/‑267) PP_4234/dsbD‑II bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2
?NC_002947_CJ‑RC 5991580 = 59 (0.920)intergenic (+59/‑487) kefB‑III/PP_mr64 glutathione‑regulated potassium/H+ antiporter/C4 ncRNA
* ? NC_002947_CJ‑RC = 48098824 (0.060)6 (0.100) 5/252 8.3 25.3% intergenic (‑288/‑267) PP_4234/dsbD‑II bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2
?NC_002947_CJ‑RC = 5991764 32 (0.530)intergenic (+243/‑303) kefB‑III/PP_mr64 glutathione‑regulated potassium/H+ antiporter/C4 ncRNA
* ? NC_002947_CJ‑RC 1737987 =76 (1.090)5 (0.080) 5/258 8.4 7.6% coding (32/348 nt) yffB glutathione‑dependent thiol reductase
?NC_002947_CJ‑RC = 1777401 55 (0.890)intergenic (+135/+157) PP_5476/PP_1585 hypothetical protein/antidote protein
* ? NC_002947_CJ‑RC = 538413549 (0.700)4 (0.080) 3/222 8.7 9.5% intergenic (+52/+81) smpB/pdhR SsrA‑binding protein/DNA‑binding transcriptional regulator LldR
?NC_002947_CJ‑RC = 5384163 39 (0.740)intergenic (+80/+53) smpB/pdhR SsrA‑binding protein/DNA‑binding transcriptional regulator LldR
* ? NC_002947_CJ‑RC = 529010222 (0.320)5 (0.080) 5/274 8.8 13.1% intergenic (‑80/+104) PP_4660/mdaB LysR family transcriptional regulator/drug activity modulator B
?NC_002947_CJ‑RC 5290245 = 46 (0.700)coding (633/672 nt) mdaB drug activity modulator B
* ? NC_002947_CJ‑RC = 56842301 (0.010)5 (0.070)
+CGGG
5/284 9.1 83.7% intergenic (‑133/+71) PP_4986/PP_4987 hemolysin III family channel protein/putative Chemotaxis protein
?NC_002947_CJ‑RC 5684231 = 1 (0.010)intergenic (‑134/+70) PP_4986/PP_4987 hemolysin III family channel protein/putative Chemotaxis protein