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 1,123,238 C→A intergenic (‑240/+64) gcvH_1 ← / ← CJ019_01062 Glycine cleavage system H protein/hypothetical protein
RA 1,309,639 C→G P2A (CCC→GCC)  aaeB_2 → p‑hydroxybenzoic acid efflux pump subunit AaeB
JC 2,191,046 +CTGAAAATATCTCTTAT intergenic (‑1/‑313) PP_RS10045 ← / → purU_3 LysR family transcriptional regulator/Formyltetrahydrofolate deformylase
RA 3,440,326 A→C S18R (AGC→CGC)  CJ019_03266 → hypothetical protein
JC 4,257,335 +GCGGCCGC intergenic (‑281/+7) CJ019_03991 ← / ← CJ019_03994 putative ABC transporter ATP‑binding protein/hypothetical protein
RA 4,759,509 G→A intergenic (+124/‑16) fpvA_3 → / → ligM_KToptimized Ferripyoverdine receptor/sequence generated by OPTIMIZER for KT2440
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
MC JC 5,389,996 Δ8 bp coding (90‑97/1666 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 87942 88059 118 22 [20] [17] 22 [CJ019_00094]–[CJ019_00095] [CJ019_00094],[CJ019_00095]
* * ÷ ACB143 674228 674396 169 24 [20] [18] 23 [nimR_1]–[mcpH_2] [nimR_1],[mcpH_2]
* * ÷ ACB143 1119632 1119715 84 23 [19] [15] 24 tdcG_2/gcvP_1 L‑serine dehydratase TdcG/Glycine dehydrogenase (decarboxylating)
* * ÷ ACB143 1376281 1376336 56 22 [21] [13] 22 CJ019_01289 hypothetical protein
* * ÷ ACB143 1396578 1396736 159 22 [14] [21] 22 [CJ019_01313]–[mcpU_1] [CJ019_01313],[mcpU_1]
* * ÷ ACB143 1499937 1500088 152 22 [21] [21] 23 [sspA] [sspA]
* * ÷ ACB143 1585616 1585700 85 22 [16] [21] 24 CJ019_01493 hypothetical protein
* * ÷ ACB143 1632585 1632688 104 22 [20] [21] 24 czcR_4/CJ019_01536 Transcriptional activator protein CzcR/hypothetical protein
* * ÷ ACB143 1696249 1696370 122 22 [19] [20] 27 lysS/CJ019_01592 Lysine‑‑tRNA ligase/hypothetical protein
* * ÷ ACB143 1705067 1705225 159 25 [21] [19] 23 ppc/adk Phosphoenolpyruvate carboxylase/Adenylate kinase
* * ÷ ACB143 2288805 2288928 124 24 [21] [21] 22 [CJ019_02172] [CJ019_02172]
* * ÷ ACB143 3046204 3046296 93 22 [21] [18] 22 [rcsC_5]–[degU_2] [rcsC_5],[degU_2]
* * ÷ ACB143 3769367 3769488 122 23 [20] [21] 22 CJ019_03581/CJ019_03582 hypothetical protein/hypothetical protein
* * ÷ ACB143 4163760 4163876 117 22 [18] [19] 27 katG/leuO_2 Catalase‑peroxidase/HTH‑type transcriptional regulator LeuO
* * ÷ ACB143 4344747 4344847 101 24 [20] [19] 23 nmoA Nitronate monooxygenase
* * ÷ ACB143 4521559 4521664 106 22 [21] [21] 23 [CJ019_04289] [CJ019_04289]
* * ÷ ACB143 4732399 4732487 89 22 [21] [21] 22 [CJ019_04468] [CJ019_04468]
* * ÷ ACB143 4845678 4845881 204 22 [21] [21] 22 recR/ybaB Recombination protein RecR/Nucleoid‑associated protein YbaB
* * ÷ ACB143 4944201 4944356 156 22 [21] [21] 22 [CJ019_04642] [CJ019_04642]
* * ÷ ACB143 5503621 5503816 196 24 [19] [21] 22 [CJ019_05176] [CJ019_05176]
* * ÷ ACB143 5534199 5534305 107 25 [18] [21] 22 [nadE] [nadE]
* * ÷ ACB143 5542267–5542753 5542753 1–487 96 [0] [21] 22 CJ019_03622 CJ019_03622
* * ÷ ACB143 5552749 5552855 107 23 [12] [21] 24 CJ019_05226/CJ019_05227 hypothetical protein/hypothetical protein
* * ÷ ACB143 5678527 5678675 149 22 [19] [21] 22 CJ019_05328/CJ019_05329 hypothetical protein/hypothetical protein
* * ÷ ACB143 5900297 5900399 103 22 [21] [21] 26 [CJ019_05521] [CJ019_05521]

Unassigned new junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? ACB143 737971 =NA (NA)37 (0.600) 26/262 1.1 92.5% coding (13/276 nt) CJ019_00701 hypothetical protein
?ACB143 1812806 = 3 (0.050)coding (995/1008 nt) rpoS RNA polymerase sigma factor RpoS
* ? ACB143 = 18128132 (0.030)59 (0.960) 34/262 0.5 96.7% coding (1002/1008 nt) rpoS RNA polymerase sigma factor RpoS
?ACB143 4527800 = NA (NA)intergenic (+730/‑85) CJ019_04293/CJ019_00703 hypothetical protein/hypothetical protein
* ? ACB143 = 55422660 (0.000)96 (1.590) 29/258 0.8 100% intergenic (‑221/+39) rpsF/CJ019_03622 30S ribosomal protein S6/IS110 family transposase ISPpu9
?ACB143 5542506 = NA (NA)intergenic (‑13/+416) CJ019_03622/rlmB IS110 family transposase ISPpu9/23S rRNA (guanosine‑2'‑O‑)‑methyltransferaseRlmB