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 1,166 T→C I389T (ATT→ACT)  dnaA → Chromosomal replication initiator protein DnaA
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 1,835,796 1 bp→TT coding (2054/2754 nt) barA ← Signal transduction histidine‑protein kinaseBarA
JC 2,191,046 +CTGAAAATATCTCTTAT intergenic (‑1/‑313) PP_RS10045 ← / → purU_3 LysR family transcriptional regulator/Formyltetrahydrofolate deformylase
RA 2,619,534 C→A Q37K (CAA→AAA)  CJ019_02478 → hypothetical protein
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 4,759,572 C→T N16N (AAC→AAT)  ligM_KToptimized → sequence generated by OPTIMIZER for KT2440
RA 5,345,991 A→C I482S (ATC→AGC)  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
RA 5,390,258 Δ2 bp coding (352‑353/1666 nt) ligH → 10‑formyltetrahydrofolate synthetase
JC 5,391,707 +54 bp intergenic (+124/‑1253) ligH → / → CJ019_05072 10‑formyltetrahydrofolate synthetase/hypothetical protein
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 87979 88059 81 23 [21] [22] 24 [CJ019_00094]–[CJ019_00095] [CJ019_00094],[CJ019_00095]
* * ÷ ACB143 161216 161470–161317 102–255 24 [20] [22] 23 [uctC_1] [uctC_1]
* * ÷ ACB143 277575 277697 123 23 [21] [21] 23 [betT2]–[tauD_2] [betT2],[tauD_2]
* * ÷ ACB143 346105 346257 153 23 [22] [22] 23 [btuD_1] [btuD_1]
* * ÷ ACB143 517190 517335 146 29 [19] [21] 24 tyrS/birA Tyrosine‑‑tRNA ligase/Bifunctional ligase/repressor BirA
* * ÷ ACB143 661102 661234 133 29 [18] [22] 30 yfhM/CJ019_00619 Alpha‑2‑macroglobulin/hypothetical protein
* * ÷ ACB143 876834 877010 177 23 [21] [22] 23 CJ019_00843/malT putative protein/HTH‑type transcriptional regulator MalT
* * ÷ ACB143 1376253 1376351 99 24 [21] [21] 23 [CJ019_01289] [CJ019_01289]
* * ÷ ACB143 1396585 1396724 140 23 [22] [22] 23 [CJ019_01313]–[mcpU_1] [CJ019_01313],[mcpU_1]
* * ÷ ACB143 1914560 1914658 99 26 [22] [22] 24 [ppsC_1]–[CJ019_01830] [ppsC_1],[CJ019_01830]
* * ÷ ACB143 1923376 1923521 146 24 [22] [21] 23 [apeB] [apeB]
* * ÷ ACB143 1940774 1940944 171 23 [22] [18] 24 [CJ019_01857] [CJ019_01857]
* * ÷ ACB143 2092933 2093072 140 23 [22] [21] 23 [rcsC_3] [rcsC_3]
* * ÷ ACB143 3046189 3046334 146 23 [21] [22] 23 [rcsC_5]–[degU_2] [rcsC_5],[degU_2]
* * ÷ ACB143 3769367 3769480 114 23 [21] [21] 24 CJ019_03581/CJ019_03582 hypothetical protein/hypothetical protein
* * ÷ ACB143 4163753 4163863 111 23 [21] [22] 23 katG/leuO_2 Catalase‑peroxidase/HTH‑type transcriptional regulator LeuO
* * ÷ ACB143 4344741 4344833 93 23 [22] [21] 23 nmoA Nitronate monooxygenase
* * ÷ ACB143 4521580 4521686 107 23 [20] [21] 24 [CJ019_04289] [CJ019_04289]
* * ÷ ACB143 4666862 4666993 132 23 [22] [21] 23 [btuB_4] [btuB_4]
* * ÷ ACB143 4732375 4732505 131 24 [20] [22] 23 [CJ019_04468] [CJ019_04468]
* * ÷ ACB143 4838411 4838564 154 23 [21] [20] 23 [CJ019_04536] [CJ019_04536]
* * ÷ ACB143 4845670 4845881 212 25 [22] [22] 23 recR/ybaB Recombination protein RecR/Nucleoid‑associated protein YbaB
* * ÷ ACB143 5090504 5090604 101 24 [22] [21] 23 argT/acs Lysine/arginine/ornithine‑binding periplasmicprotein/Acetyl‑coenzyme A synthetase
* * ÷ ACB143 5250121 5250228 108 23 [22] [22] 31 [CJ019_04947]–[CJ019_04948] [CJ019_04947],[CJ019_04948]
* * ÷ ACB143 5482273 5482407 135 23 [22] [22] 23 [purH] [purH]
* * ÷ ACB143 5503622 5503853 232 23 [21] [22] 23 [CJ019_05176] [CJ019_05176]
* * ÷ ACB143 5554961 5555171 211 24 [22] [20] 23 [purA] [purA]
* * ÷ ACB143 5900294 5900411 118 24 [21] [20] 26 [CJ019_05521] [CJ019_05521]

Unassigned new junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? ACB143 2155685 =47 (0.710)61 (0.920) 32/260 0.7 53.3% coding (301/369 nt) tmk_1 Thymidylate kinase
?ACB143 = 2220562 60 (0.910)coding (36/369 nt) tmk_2 Thymidylate kinase