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‑RC1,070,2462.A66.7% 50.0 / 32.8 30intergenic (+46/+96)aroP‑I/PP_0928aromatic amino acid transport protein/K+‑dependent Na+/Ca+ exchanger‑like protein
*NC_002947_CJ‑RC1,070,2461.G63.0% 26.8 / 31.8 30intergenic (+46/+96)aroP‑I/PP_0928aromatic amino acid transport protein/K+‑dependent Na+/Ca+ exchanger‑like protein
*NC_002947_CJ‑RC697,0940AG57.9% ‑3.1 / 14.6 22intergenic (+21/‑730)mmsA‑I/PP_16SDmethylmalonate‑semialdehyde dehydrogenase/16S ribosomal RNA
*NC_002947_CJ‑RC4,353,2900CG55.6% 2.3 / 10.1 9G103G (GGC→GGGyrpB2‑nitropropane dioxygenase
*NC_002947_CJ‑RC697,1070TG55.0% ‑3.3 / 12.0 23intergenic (+34/‑717)mmsA‑I/PP_16SDmethylmalonate‑semialdehyde dehydrogenase/16S ribosomal RNA
*NC_002947_CJ‑RC699,7220AG54.3% 6.4 / 121.5 94intergenic (+115/‑129)PP_t06/PP_23SDtRNA‑Ala/23S ribosomal RNA
*NC_002947_CJ‑RC4,348,8120AG52.0% 14.7 / 139.9 102intergenic (‑70/+404)PP_3820/galUgroup II intron‑encoding maturase/UTP‑glucose‑1‑phosphate uridylyltransferase
*NC_002947_CJ‑RC1,327,1210CT47.9% 98.3 / 227.9 165intergenic (+97/‑196)PP_16SE/PP_23SE16S ribosomal RNA/23S ribosomal RNA
*NC_002947_CJ‑RC2,737,1090TG39.0% 51.4 / 18.8 41V1336G (GTG→GGG) PP_2394leucine‑rich repeat‑containing protein
*NC_002947_CJ‑RC5,773,9490TG38.6% 63.8 / 12.1 44E610A (GAG→GCG) betT‑Icholine transporter
*NC_002947_CJ‑RC3,447,2860AC36.8% 22.4 / 10.1 41S18R (AGC→CGC) PP_5556bacteriophage lysis protein
*NC_002947_CJ‑RC2,954,6530AG35.7% 28.9 / 10.2 29intergenic (‑156/‑125)PP_2586/PP_2587putative amino acid transporter/LuxR family transcriptional regulator
*NC_002947_CJ‑RC3,171,7740AT34.3% 29.6 / 12.7 35I16F (ATT→TTT) PP_2784short‑chain dehydrogenase/reductase family oxidoreductase
*NC_002947_CJ‑RC1,403,5910TC28.6% 18.5 / 10.5 25intergenic (‑57/+24)PP_1227/PP_1228membrane protein/methyl‑accepting chemotaxis transducer
*NC_002947_CJ‑RC6,048,0010AC27.9% 84.6 / 10.8 43V35G (GTG→GGG) PP_5297amino acid transporter
*NC_002947_CJ‑RC131,2620CT27.0% 121.2 / 46.2 74K4K (AAG→AAAengBGTP‑binding protein
*NC_002947_CJ‑RC3,516,0640AC26.9% 93.0 / 11.8 52intergenic (+104/‑1031)PP_5576/PP_5578hypothetical protein/hypothetical protein
*NC_002947_CJ‑RC2,282,7700TG26.1% 32.6 / 10.8 23intergenic (‑162/+67)PP_2010/PP_2011cytochrome b561/hypothetical protein
*NC_002947_CJ‑RC3,578,4330GT25.7% 66.3 / 11.2 35intergenic (+110/‑214)PP_3158/PP_5589hypothetical protein/rhs repeat‑associated core domain‑containing protein
*NC_002947_CJ‑RC441,3260G.25.6% 108.5 / 36.7 44coding (207/1173 nt)bioF8‑amino‑7‑oxononanoate synthase

Marginal new junction evidence (lowest skew 10 of 33 shown)
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NC_002947_CJ‑RC = 65278248 (0.690)12 (0.200) 11/250 6.2 36.7% coding (1961/1962 nt) ctpL methyl‑accepting chemotaxis protein CtpL
?NC_002947_CJ‑RC = 4809862 0 (0.000)intergenic (‑268/‑287) PP_4234/dsbD‑II bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2
* ? NC_002947_CJ‑RC = 295708035 (0.510)12 (0.180) 12/280 6.7 26.2% intergenic (+35/‑161) PP_2588/PP_2589 class III aminotransferase/aldehyde dehydrogenase family protein
?NC_002947_CJ‑RC 2957165 = 34 (0.510)intergenic (+120/‑76) PP_2588/PP_2589 class III aminotransferase/aldehyde dehydrogenase family protein
* ? NC_002947_CJ‑RC = 48098823 (0.040)9 (0.150) 9/250 7.1 30.2% intergenic (‑288/‑267) PP_4234/dsbD‑II bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2
?NC_002947_CJ‑RC = 5991764 39 (0.650)intergenic (+243/‑303) kefB‑III/PP_mr64 glutathione‑regulated potassium/H+ antiporter/C4 ncRNA
* ? NC_002947_CJ‑RC = 55584232 (0.030)11 (0.160)
+GCC
11/284 7.2 84.9% 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 = 45861369 (0.130)14 (0.220) 9/268 7.6 49.7% intergenic (+112/+103) PP_4061/PP_4063 hypothetical protein/long‑chain fatty acid‑‑CoA ligase
?NC_002947_CJ‑RC = 4586216 20 (0.310)intergenic (+192/+23) PP_4061/PP_4063 hypothetical protein/long‑chain fatty acid‑‑CoA ligase
* ? NC_002947_CJ‑RC = 56842304 (0.060)11 (0.160)
+CGGG
9/282 8.0 73.9% intergenic (‑133/+71) PP_4986/PP_4987 hemolysin III family channel protein/putative Chemotaxis protein
?NC_002947_CJ‑RC 5684231 = 4 (0.060)intergenic (‑134/+70) PP_4986/PP_4987 hemolysin III family channel protein/putative Chemotaxis protein
* ? NC_002947_CJ‑RC 4809877 =6 (0.090)8 (0.150) 5/220 8.3 29.9% intergenic (‑283/‑272) PP_4234/dsbD‑II bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2
?NC_002947_CJ‑RC = 5991750 33 (0.630)intergenic (+229/‑317) kefB‑III/PP_mr64 glutathione‑regulated potassium/H+ antiporter/C4 ncRNA
* ? NC_002947_CJ‑RC = 247214033 (0.480)4 (0.080) 4/212 8.6 17.7% intergenic (+44/+105) PP_2166/PP_2167 anti‑anti‑sigma factor/PhoD‑like phosphatase
?NC_002947_CJ‑RC = 2472186 13 (0.260)intergenic (+90/+59) PP_2166/PP_2167 anti‑anti‑sigma factor/PhoD‑like phosphatase
* ? NC_002947_CJ‑RC 5384101 =26 (0.380)4 (0.080) 3/220 9.7 20.7% intergenic (+18/+115) smpB/pdhR SsrA‑binding protein/DNA‑binding transcriptional regulator LldR
?NC_002947_CJ‑RC 5384199 = 11 (0.210)intergenic (+116/+17) smpB/pdhR SsrA‑binding protein/DNA‑binding transcriptional regulator LldR
* ? NC_002947_CJ‑RC = 570155822 (0.320)4 (0.070) 4/256 10.1 17.6% intergenic (+33/‑134) hslU/PP_5002 protease HslVU ATPase subunit/hypothetical protein
?NC_002947_CJ‑RC = 5701607 18 (0.290)intergenic (+82/‑85) hslU/PP_5002 protease HslVU ATPase subunit/hypothetical protein