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

Predicted mutations
evidence position mutation annotation gene description
MC JC 257,908 Δ776 bp [crl] [crl]
RA 1,529,175 T→C pseudogene (1274/2037 nt) rhsE → pseudogene, Rhs family
RA 1,529,180 T→C pseudogene (1279/2037 nt) rhsE → pseudogene, Rhs family
RA 1,529,185 C→T pseudogene (1284/2037 nt) rhsE → pseudogene, Rhs family
RA 1,529,203 C→A pseudogene (1302/2037 nt) rhsE → pseudogene, Rhs family
RA 1,529,218 C→T pseudogene (1317/2037 nt) rhsE → pseudogene, Rhs family
RA 2,173,363 Δ2 bp intergenic (‑1/+1) gatC ← / ← gatC pseudogene, galactitol‑specific enzyme IIC component of PTS;transport; Transport of small molecules: Carbohydrates, organic acids, alcohols; PTS system galactitol‑specific enzyme IIC/pseudogene, galactitol‑specific enzyme IIC component of PTS;transport; Transport of small molecules: Carbohydrates, organic acids, alcohols; PTS system galactitol‑specific enzyme IIC
RA 3,560,455 +G intergenic (‑2/+1) glpR ← / ← glpR pseudogene, DNA‑binding transcriptional repressor;regulator; Energy metabolism, carbon: Anaerobic respiration; repressor of the glp operon/pseudogene, DNA‑binding transcriptional repressor;regulator; Energy metabolism, carbon: Anaerobic respiration; repressor of the glp operon
RA 3,937,351 A→T N20Y (AAT→TAT)  rbsK → ribokinase
JC JC 3,938,845 IS2 (+) +5 bp coding (619‑623/993 nt) rbsR → transcriptional repressor of ribose metabolism
RA 4,296,381 +GC intergenic (+587/+55) gltP → / ← yjcO glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein

Unassigned missing coverage evidence
   seq id start end size ←reads reads→ gene description
* * ÷ NC_000913 527349 528325 977 30 [28] [26] 31 [rhsD]–[rhsH] [rhsD],ybbC,[rhsH]
* * ÷ NC_000913 582740 584689 1950 29 [28] [27] 30 [ybcY]–[ompT] [ybcY],ybcY,tfaX,appY,[ompT]
* * ÷ NC_000913 1215516 1215762 247 30 [28] [26] 32 bluF/ycgZ anti‑repressor for YcgE, blue light‑responsive; FAD‑binding; inactive c‑di‑GMP phosphodiesterase‑like EAL domain protein/RcsB connector protein for regulation of biofilm and acid‑resistance
* * ÷ NC_000913 1299386 1300764 1379 29 [28] [27] 31 ychE/oppA UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein
* * ÷ NC_000913 1529972 1530477 506 30 [28] [28] 31 [ydcD] [ydcD]
* * ÷ NC_000913 1632618 1633622–1633621 1004–1005 30 [28] [28] 33 ydfK–[pinQ] ydfK,[pinQ]
* * ÷ NC_000913 1812675 1813352 678 29 [27] [28] 29 [ydjO] [ydjO]
* * ÷ NC_000913 1946041 1946304 264 29 [28] [27] 29 yobI–[yebB] yobI,[yebB]
* * ÷ NC_000913 1978398 1979687 1290 31 [26] [26] 30 insB1–insA insB1,insA
* * ÷ NC_000913 2033495 2034142 648 30 [26] [27] 29 rseX–[yedS] rseX,[yedS]
* * ÷ NC_000913 2469102 2470742 1641 29 [27] [26] 30 [gtrB]–gtrS [gtrB],gtrS
* * ÷ NC_000913 2773282 2773987 706 30 [28] [28] 29 [yfjW] [yfjW]
* * ÷ NC_000913 2995030 2995513 484 29 [27] [28] 30 [ygeK]–[ygeN] [ygeK],[ygeN]
* * ÷ NC_000913 3423855–3424478 3424478 1–624 29 [27] [28] 30 [rrlD] [rrlD]
* * ÷ NC_000913 3581688 3582213 526 29 [28] [28] 35 [yhhZ] [yhhZ]
* * ÷ NC_000913 3798993 3799507 515 30 [28] [23] 33 [waaU]–[waaZ] [waaU],[waaZ]
* * ÷ NC_000913 4251429 4252073 645 29 [28] [27] 32 yjbI pseudogene, SopA‑related, pentapeptide repeats‑containing
* * ÷ NC_000913 4476471 4477233 763 35 [27] [28] 29 yjgL SopA‑central‑domain‑like hexapeptide repeat protein

Unassigned new junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NC_000913 1207790 =13 (0.140)65 (0.760) 48/494 0.5 83.8% coding (290/630 nt) stfP e14 prophage; uncharacterized protein
?NC_000913 1209619 = 13 (0.150)pseudogene (1/501 nt) stfE pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
* ? NC_000913 = 120780513 (0.140)54 (0.630) 44/494 0.7 81.1% coding (305/630 nt) stfP e14 prophage; uncharacterized protein
?NC_000913 = 1209602 13 (0.150)pseudogene (18/501 nt) stfE pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related