breseq  version 0.39.0  
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 insB9–[crl] insB9, insA9, [crl]
RA 557,635 A→T L36Q (CTG→CAG)  folD ← bifunctional methylenetetrahydrofolate dehydrogenase/methenyltetrahydrofolate cyclohydrolase
RA 1,065,278 C→T R415C (CGT→TGT)  yccE → uncharacterized protein YccE
JC JC 1,105,376 IS2 (–) +5 bp intergenic (+83/‑34) csgC → / → ymdA curlin chaperone/uncharacterized protein YmdA
RA 1,301,998 A→G S273G (AGC→GGC)  oppA → oligopeptide ABC transporter periplasmic binding protein
RA 1,337,394 A→G S522G (AGC→GGC)  acnA → aconitate hydratase 1
MC JC 1,397,239 Δ7,315 bp IS5‑mediated ynaJ–[abgA] ynaJ, uspE, fnr, ogt, abgT, abgB, [abgA]
RA 1,652,331 T→C intergenic (+2346/+397) ydfD → / ← ynfP lysis protein/protein YnfP
RA 1,737,584 A→G intergenic (‑39/‑260) cydH ← / → purR cytochrome bd‑I accessory subunit CydH/DNA‑binding transcriptional repressor PurR
RA 2,032,423 G→A V219V (GTC→GTT)  yedJ ← putative HD superfamily phosphohydrolase YedJ
RA 2,173,363 Δ2 bp intergenic (‑490/+918) gatD ← / ← gatB galactitol‑1‑phosphate 5‑dehydrogenase/galactitol‑specific PTS enzyme IIB component
JC JC 2,406,780 IS1 (–) +8 bp intergenic (‑139/‑774) lrhA ← / → alaA DNA‑binding transcriptional dual regulator LrhA/glutamate‑‑pyruvate aminotransferase AlaA
RA 2,867,453 C→A Q33Y (CAG→TAT)  rpoS ← RNA polymerase sigma factor RpoS
RA 2,867,455 G→A Q33Y (CAG→TAT)  rpoS ← RNA polymerase sigma factor RpoS
RA 2,908,319 C→G D450H (GAC→CAC)  pyrG ← CTP synthetase
RA 3,486,205 C→A T29K (ACG→AAG)  crp → DNA‑binding transcriptional dual regulator CRP
RA 3,560,455 +G intergenic (+589/+167) rtcR → / ← glpG DNA‑binding transcriptional activator RtcR/rhomboid protease GlpG
JC JC 3,890,892 IS1 (+) +9 bp coding (657‑665/1248 nt) tnaB → tryptophan:H(+) symporter TnaB
RA 3,980,226 G→A V91I (GTT→ATT)  rffM → UDP‑N‑acetyl‑D‑mannosaminuronic acid transferase
RA 4,296,381 +GC intergenic (+587/+55) gltP → / ← yjcO glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO
JC JC 4,366,110 IS1 (+) +8 bp coding (657‑664/1302 nt) dcuA ← C4‑dicarboxylate transporter DcuA

Unassigned missing coverage evidence
   seq id start end size ←reads reads→ gene description
* * ÷ NC_000913 119176 119204 29 2 [0] [1] 2 ampD 1,6‑anhydro‑N‑acetylmuramoyl‑L‑alanine amidase
* * ÷ NC_000913 164578 164634 57 2 [1] [0] 2 hrpB/mrcB RNA‑dependent NTPase HrpB/peptidoglycan glycosyltransferase/peptidoglycan DD‑transpeptidase MrcB
* * ÷ NC_000913 755482 755504 23 2 [1] [0] 2 sdhC succinate:quinone oxidoreductase, membrane protein SdhC
* * ÷ NC_000913 1299499–1300692 1300692 1–1194 20 [0] [1] 2 insH21 insH21
* * ÷ NC_000913 1411925 1414842 2918 11 [0] [0] 2 [ttcA]–[recE] [ttcA],intR,xisR,rcbA,ralA,ralR,recT,[recE]
* * ÷ NC_000913 1414950 1422883 7934 2 [1] [1] 2 [recE]–[ydaW] [recE],racC,ydaE,kilR,kilS,sieB,ydaF,ydaG,racR,ydaS,ydaT,ydaU,ydaV,[ydaW]
* * ÷ NC_000913 1423072 1430190 7119 2 [0] [1] 2 [ydaW]–[stfR] [ydaW],rzoR,trkG,ynaK,ydaY,ynaA,lomR,insH5,lomR,[stfR]
* * ÷ NC_000913 1430352 1434984 4633 2 [1] [1] 12 [stfR]–ynaM [stfR],tfaR,pinR,ynaE,ynaM
* * ÷ NC_000913 1978495 1979270 776 10 [0] [0] 17 insB5–insA5 insB5,insA5
* * ÷ NC_000913 2134951 2135107 157 2 [1] [1] 2 wzc protein‑tyrosine kinase Wzc
* * ÷ NC_000913 3045995 3046066 72 2 [1] [1] 2 ygfF/gcvP putative oxidoreductase YgfF/glycine decarboxylase
* * ÷ NC_000913 3239533 3239638 106 2 [1] [1] 2 [alx] [alx]
* * ÷ NC_000913 3362975 3362995 21 2 [1] [1] 2 yhcD putative fimbrial usher protein YhcD
* * ÷ NC_000913 3423885–3424234 3424457–3424248 15–573 2 [1] [1] 2 rrlD 23S ribosomal RNA
* * ÷ NC_000913 3439592 3439660 69 2 [1] [1] 2 [rplQ] [rplQ]
* * ÷ NC_000913 3608613 3608727 115 2 [1] [1] 2 [zntA] [zntA]
* * ÷ NC_000913 3727218 3727271 54 2 [1] [1] 2 yiaA PF05360 family inner membrane protein YiaA
* * ÷ NC_000913 3781087 3781122 36 2 [1] [1] 2 lldD/trmL L‑lactate dehydrogenase/tRNA (cytidine/uridine‑2'‑O)‑ribose methyltransferase
* * ÷ NC_000913 4341230 4341235 6 2 [1] [1] 2 melR DNA‑binding transcriptional dual regulator MelR
* * ÷ NC_000913 4549725 4549777 53 2 [1] [1] 2 fimH/gntP type 1 fimbriae D‑mannose specific adhesin/fructuronate transporter

Unassigned new junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NC_000913 = 12994981 (0.090)19 (1.630) 18/286 0.0 95.0% intergenic (+253/‑69) ychE/insH21 MarC family putative inner membrane protein YchE/IS5 family transposase and trans‑activator
?NC_000913 = 1300693 NA (NA)noncoding (1195/1195 nt) IS5 repeat region
* ? NC_000913 1299499 =NA (NA)17 (1.460) 14/286 0.0 100% noncoding (1/1195 nt) IS5 repeat region
?NC_000913 1300694 = 0 (0.000)intergenic (+147/‑488) insH21/oppA IS5 family transposase and trans‑activator/oligopeptide ABC transporter periplasmic binding protein
* ? NC_000913 = 1397238NA (NA)10 (0.790) 9/310 0.2 100% noncoding (1195/1195 nt) IS5 repeat region
?NC_000913 = 1978494 0 (0.000)intergenic (‑297/+24) flhD/insB5 DNA‑binding transcriptional dual regulator FlhD/IS1 family protein InsB
* ? NC_000913 = 14119240 (0.000)11 (1.050) 10/258 0.1 100% coding (25/936 nt) ttcA tRNA cytosine(32) 2‑sulfurtransferase TtcA
?NC_000913 1434985 = 0 (0.000)intergenic (‑579/+200) ynaM/uspF protein YnaM/universal stress protein F
* ? NC_000913 1979271 =0 (0.000)17 (1.350) 15/310 0.0 100% intergenic (‑56/‑482) insA5/uspC IS1 family protein InsA/universal stress protein C
?NC_000913 = 2102947 NA (NA)pseudogene (443/446 nt) wbbL interrupted rhamnosyltransferase WbbL