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

Predicted mutations
evidence position mutation annotation gene description
RA 44,301 (T)9→8 intergenic (+132/‑359) oprD_1 → / → czcR_2 Porin D/Transcriptional activator protein CzcR
RA 120,983 (T)9→8 intergenic (+280/+92) polA → / ← engB DNA polymerase I/putative GTP‑binding protein EngB
RA 179,484 T→C C316R (TGC→CGC)  CJ019_00182 → hypothetical protein
RA 1,310,041 (C)5→6 coding (406/1989 nt) aaeB_2 → p‑hydroxybenzoic acid efflux pump subunit AaeB
RA 2,143,429 C→T E50K (GAA→AAA)  rne ← Ribonuclease E
JC 2,191,046 +CTGAAAATATCTCTTAT intergenic (‑1/‑313) PP_RS10045 ← / → purU_3 LysR family transcriptional regulator/Formyltetrahydrofolate deformylase
RA 2,626,199 Δ2 bp coding (75‑76/273 nt) hupB_2 → DNA‑binding protein HU‑beta
JC 4,257,335 +GCGGCCGC intergenic (‑281/+7) CJ019_03991 ← / ← CJ019_03994 putative ABC transporter ATP‑binding protein/hypothetical protein
RA 4,759,531 G→T A3S (GCC→TCC)  ligM_KToptimized → sequence generated by OPTIMIZER for KT2440
JC 4,901,237 (CCGTTG)5→4 coding (99‑104/198 nt) CJ019_04595 ← hypothetical protein
RA 5,345,970 A→G L489P (CTG→CCG)  pnp ← Polyribonucleotide nucleotidyltransferase
RA 5,386,500 C→A intergenic (‑509/+1142) CJ019_05070 ← / ← nptII hypothetical protein/neomycin phosphotransferase
RA 5,386,503 C→G intergenic (‑512/+1139) CJ019_05070 ← / ← nptII hypothetical protein/neomycin phosphotransferase
RA 5,386,506 1 bp→GT intergenic (‑515/+1136) CJ019_05070 ← / ← nptII hypothetical protein/neomycin phosphotransferase
RA 5,386,507 +C intergenic (‑516/+1135) CJ019_05070 ← / ← nptII hypothetical protein/neomycin phosphotransferase
RA 5,386,510 2 bp→TA intergenic (‑519/+1131) CJ019_05070 ← / ← nptII hypothetical protein/neomycin phosphotransferase
RA 5,386,513 +AA intergenic (‑522/+1129) CJ019_05070 ← / ← nptII hypothetical protein/neomycin phosphotransferase
RA 5,386,514 T→C intergenic (‑523/+1128) CJ019_05070 ← / ← nptII hypothetical protein/neomycin phosphotransferase
RA 5,386,517 G→C intergenic (‑526/+1125) CJ019_05070 ← / ← nptII hypothetical protein/neomycin phosphotransferase
RA 5,386,519 G→A intergenic (‑528/+1123) CJ019_05070 ← / ← nptII hypothetical protein/neomycin phosphotransferase
RA 5,386,811 C→T intergenic (‑820/+831) CJ019_05070 ← / ← nptII hypothetical protein/neomycin phosphotransferase
JC 5,390,915 (GCTCA)1→2 coding (1009/1666 nt) ligH → 10‑formyltetrahydrofolate synthetase
RA 5,760,598 (A)6→5 coding (781/834 nt) CJ019_05400 → hypothetical protein

Unassigned missing coverage evidence
   seq id start end size ←reads reads→ gene description
* * ÷ ACB143 87964 88059 96 20 [18] [19] 23 [CJ019_00094]–[CJ019_00095] [CJ019_00094],[CJ019_00095]
* * ÷ ACB143 517191 517324 134 20 [19] [19] 20 tyrS/birA Tyrosine‑‑tRNA ligase/Bifunctional ligase/repressor BirA
* * ÷ ACB143 674245 674385 141 24 [18] [19] 23 [nimR_1]–[mcpH_2] [nimR_1],[mcpH_2]
* * ÷ ACB143 711474 711558 85 20 [18] [16] 20 [thiO]–[aam] [thiO],[aam]
* * ÷ ACB143 908050 908244 195 20 [19] [19] 20 [fruA]–[CJ019_00870] [fruA],[CJ019_00870]
* * ÷ ACB143 1585580 1585716 137 21 [17] [19] 23 CJ019_01493 hypothetical protein
* * ÷ ACB143 1697637 1697755 119 20 [18] [19] 20 [CJ019_01593]–[CJ019_01594] [CJ019_01593],[CJ019_01594]
* * ÷ ACB143 1914570 1914664 95 22 [17] [16] 20 [ppsC_1]–[CJ019_01830] [ppsC_1],[CJ019_01830]
* * ÷ ACB143 1923378 1923542 165 20 [18] [18] 24 [apeB] [apeB]
* * ÷ ACB143 1940781 1940928 148 20 [18] [19] 20 [CJ019_01857] [CJ019_01857]
* * ÷ ACB143 2288798 2288917 120 20 [17] [15] 22 CJ019_02171/CJ019_02172 hypothetical protein/hypothetical protein
* * ÷ ACB143 3046177 3046335 159 21 [19] [19] 20 [rcsC_5]–[degU_2] [rcsC_5],[degU_2]
* * ÷ ACB143 3839275 3839414 140 20 [19] [19] 21 [argP_2] [argP_2]
* * ÷ ACB143 4025724 4025820 97 31 [19] [19] 20 [dmdC_5] [dmdC_5]
* * ÷ ACB143 4330036 4330137 102 20 [14] [19] 23 [CJ019_04068] [CJ019_04068]
* * ÷ ACB143 4344747 4344827 81 20 [19] [19] 20 nmoA Nitronate monooxygenase
* * ÷ ACB143 4521582 4521685 104 21 [19] [19] 20 [CJ019_04289] [CJ019_04289]
* * ÷ ACB143 4666874 4666991 118 20 [16] [19] 20 [btuB_4] [btuB_4]
* * ÷ ACB143 4732381 4732518 138 20 [18] [17] 20 [CJ019_04468] [CJ019_04468]
* * ÷ ACB143 4845672 4845891 220 24 [18] [18] 20 recR/ybaB Recombination protein RecR/Nucleoid‑associated protein YbaB
* * ÷ ACB143 4944216 4944366 151 21 [19] [19] 21 [CJ019_04642] [CJ019_04642]
* * ÷ ACB143 5192906 5193034 129 22 [17] [19] 20 [gltR_4]–[CJ019_04888] [gltR_4],[CJ019_04888]
* * ÷ ACB143 5250102 5250222 121 21 [18] [16] 21 [CJ019_04947]–[CJ019_04948] [CJ019_04947],[CJ019_04948]
* * ÷ ACB143 5474243 5474393 151 21 [19] [18] 20 [CJ019_05147]–[CJ019_05148] [CJ019_05147],[CJ019_05148]
* * ÷ ACB143 5503645 5503836 192 20 [19] [17] 21 [CJ019_05176] [CJ019_05176]
* * ÷ ACB143 5900297 5900399 103 20 [19] [18] 27 [CJ019_05521] [CJ019_05521]

Unassigned new junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? ACB143 1837190 =0 (0.000)63 (1.150) 32/252 0.3 65.6% coding (660/2754 nt) barA Signal transduction histidine‑protein kinaseBarA
?ACB143 = 2172433 66 (1.210)intergenic (+175/+93) CJ019_02060/CJ019_02061 IS1182 family transposase ISPpu16/hypothetical protein
* ? ACB143 = 18371930 (0.000)39 (0.710) 27/254 0.6 72.9% coding (657/2754 nt) barA Signal transduction histidine‑protein kinaseBarA
?ACB143 2170759 = 29 (0.530)intergenic (‑774/‑63) arsR1/CJ019_02060 Arsenic resistance transcriptional regulatorArsR1/IS1182 family transposase ISPpu16