breseq  version 0.33.1  revision 8505477f25b3
mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Marginal read alignment evidence
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE512,6430AG48.7% 48.9 / inf 263intergenic (+711/‑6052)recR/speA_2Recombination protein RecR/Arginine decarboxylase
*USA300TCH1516_ALE111,5120AG33.5% 248.7 / 194.4 212S194S (TCA→TCG) USA300HOU_RS00520putative lipoprotein
*USA300TCH1516_ALE111,5160CA32.8% 336.0 / 188.1 204Q196K (CAA→AAA) USA300HOU_RS00520putative lipoprotein

Marginal new junction evidence (lowest skew 10 of 144 shown)
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? CP000731 = 443310 (2.380)27 (0.020) 9/260 0.0 2.2% intergenic (+398/‑67) USA300HOU_pUSA300HOUMR0006/cadR hypothetical protein/cadmium binding protein
?NC_012417 = 1931 2433 (0.860)intergenic (+164/+162) USA300HOU_RS14895/USA300HOU_RS14900 hypothetical protein/hypothetical protein
* ? CP000731 = 441911 (2.610)25 (0.020) 16/254 0.0 2.0% intergenic (+384/‑81) USA300HOU_pUSA300HOUMR0006/cadR hypothetical protein/cadmium binding protein
?NC_012417 = 1946 2408 (0.870)intergenic (+179/+147) USA300HOU_RS14895/USA300HOU_RS14900 hypothetical protein/hypothetical protein
* ? CP000731 = 438110 (2.380)54 (0.040) 21/256 0.0 4.1% intergenic (+346/‑119) USA300HOU_pUSA300HOUMR0006/cadR hypothetical protein/cadmium binding protein
?NC_012417 = 1975 2506 (0.900)intergenic (+208/+118) USA300HOU_RS14895/USA300HOU_RS14900 hypothetical protein/hypothetical protein
* ? CP000731 4323 =4 (0.950)28 (0.020) 17/256 0.0 2.3% intergenic (+288/‑177) USA300HOU_pUSA300HOUMR0006/cadR hypothetical protein/cadmium binding protein
?NC_012417 2035 = 2367 (0.850)intergenic (+268/+58) USA300HOU_RS14895/USA300HOU_RS14900 hypothetical protein/hypothetical protein
* ? CP000731 4294 =4 (0.950)75 (0.050) 29/254 0.0 6.1% intergenic (+259/‑206) USA300HOU_pUSA300HOUMR0006/cadR hypothetical protein/cadmium binding protein
?NC_012417 2073 = 2319 (0.840)intergenic (+306/+20) USA300HOU_RS14895/USA300HOU_RS14900 hypothetical protein/hypothetical protein
* ? CP000731 = 16102 (0.480)65 (0.050) 21/250 0.0 4.8% intergenic (+395/‑461) repA/USA300HOU_pUSA300HOUMR0003 replication protein A/hypothetical protein
?NC_012417 = 1047 2570 (0.940)coding (148/192 nt) USA300HOU_RS15665 hypothetical protein
* ? USA300TCH1516_ALE = 120532394 (0.750)59 (0.660)
+38 bp		 16/194 6.9 43.5% intergenic (‑204/‑365) USA300HOU_RS15290/lspA hypothetical protein/Lipoprotein signal peptidase
?USA300TCH1516_ALE = 2072043 119 (0.950)intergenic (+538/+35) USA300HOU_RS10445/USA300HOU_RS10450 hypothetical protein/hypothetical protein
* ? USA300TCH1516_ALE = 120532394 (0.750)59 (0.660)
+38 bp		 16/194 6.9 46.6% intergenic (‑204/‑365) USA300HOU_RS15290/lspA hypothetical protein/Lipoprotein signal peptidase
?USA300TCH1516_ALE = 1443739 NA (NA)intergenic (‑312/+41) USA300TCH1516_01342/brnQ_3 hypothetical protein/Branched‑chain amino acid transport system 2 carrier protein
* ? USA300TCH1516_ALE = 120532394 (0.750)58 (0.650)
+38 bp		 15/194 7.2 43.2% intergenic (‑204/‑365) USA300HOU_RS15290/lspA hypothetical protein/Lipoprotein signal peptidase
?USA300TCH1516_ALE 2478252 = 118 (0.940)intergenic (+139/‑436) USA300HOU_RS12760/USA300HOU_RS12765 hypothetical protein/hypothetical protein
* ? USA300TCH1516_ALE = 120532394 (0.750)58 (0.650)
+38 bp		 15/194 7.2 45.7% intergenic (‑204/‑365) USA300HOU_RS15290/lspA hypothetical protein/Lipoprotein signal peptidase
?USA300TCH1516_ALE 1426517 = 98 (0.780)intergenic (‑248/+724) pstS/cvfB Phosphate‑binding protein PstS/Conserved virulence factor B