mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.32.1 revision aa8f2595a244
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Predicted mutations | |||||
|---|---|---|---|---|---|
| evidence | position | mutation | annotation | gene | description |
| RA | 219,650 | G→A | P116S (CCA→TCA) | rcsF ← | putative outer membrane protein |
| MC JC | 257,908 | Δ776 bp | [crl] | [crl] | |
| RA | 287,971 | A→G | T395A (ACG→GCG) | yagH → | CP4‑6 prophage, putative xylosidase/arabinosidase |
| RA | 322,417 | T→A | V27E (GTG→GAG) | ykgF → | ferridoxin‑like LutB family protein, putative electron transport chain YkgEFG component |
| RA | 573,440 | C→T | R24C (CGC→TGC) | rusA → | DLP12 prophage, endonuclease RUS |
| RA | 738,241 | T→C | F50F (TTT→TTC) | ybfD → | H repeat‑associated putative transposase |
| RA | 764,978 | G→A | E267K (GAA→AAA) | sucD → | succinyl‑CoA synthetase, NAD(P)‑binding, alpha subunit |
| RA | 786,791 | C→T | intergenic (+106/+52) | aroG → / ← gpmA | 3‑deoxy‑D‑arabino‑heptulosonate‑7‑phosphate synthase, phenylalanine repressible/phosphoglyceromutase 1 |
| RA | 1,037,464 | A→G | D239G (GAC→GGC) | hyaF → | hydrogenase‑1 protein nickel incorporation factor |
| RA | 1,065,209 | C→T | P392S (CCT→TCT) | yccE → | uncharacterized protein |
| RA | 1,097,218 | (G)7→8 | intergenic (+389/+347) | ycdU → / ← serX | putative inner membrane protein/tRNA‑Ser |
| RA | 1,104,949 | C→T | intergenic (+47/‑12) | csgA → / → csgC | curlin subunit, amyloid curli fibers, cryptic/curli assembly protein |
| RA | 1,176,078 | A→G | N218D (AAT→GAT) | lolC → | lipoprotein‑releasing system transmembrane protein |
| RA | 1,287,826 | C→T | A267T (GCA→ACA) | purU ← | formyltetrahydrofolate hydrolase |
| MC JC | 1,299,499 | Δ1,199 bp | intergenic (+254/‑485) | ychE → / → oppA | UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein |
| RA | 1,414,019 | C→T | G259R (GGG→AGG) | recT ← | Rac prophage, recombination and repair protein |
| RA | 1,458,617 | A→G | A118A (GCA→GCG) | paaG → | 1,2‑epoxyphenylacetyl‑CoA isomerase, oxepin‑CoA‑forming |
| RA | 1,594,132 | (C)8→10 | pseudogene (3856/3861 nt) | yneO ← | pseudogene, AidA homolog |
| RA | 1,595,427 | A→G | pseudogene (2561/3861 nt) | yneO ← | pseudogene, AidA homolog |
| RA | 1,756,464 | T→C | V256A (GTT→GCT) | pykF → | pyruvate kinase I |
| RA | 1,792,702 | T→C | A10A (GCA→GCG) | nlpC ← | putative C40 clan peptidase lipoprotein |
| RA | 1,904,586 | T→C | V231A (GTC→GCC) | manZ → | mannose‑specific enzyme IID component of PTS |
| RA | 1,907,417 | G→A | Q7* (CAG→TAG) | cspC ← | stress protein, member of the CspA‑family |
| RA | 1,907,713 | (T)7→8 | intergenic (‑122/+548) | yobF ← / ← yebO | DUF2527 family heat‑induced protein/putative inner membrane protein |
| RA | 1,927,241 | (C)6→7 | coding (1599/2061 nt) | ptrB ← | protease II |
| RA | 1,939,718 | G→A | A159V (GCG→GTG) | lpxM ← | myristoyl‑acyl carrier protein (ACP)‑dependent acyltransferase |
| RA | 1,968,408 | C→T | V32M (GTG→ATG) | cheB ← | fused chemotaxis regulator: protein‑glutamate methylesterase in two‑component regulatory system with CheA |
| RA | 1,971,962 | G→A | R244C (CGC→TGC) | tar ← | methyl‑accepting chemotaxis protein II |
| MC JC | 1,978,503 | Δ776 bp | insB1–insA | insB1, insA | |
| RA | 2,072,659 | G→A | G374D (GGC→GAC) | flu → | CP4‑44 prophage, antigen 43 (Ag43) phase‑variable biofilm formation autotransporter |
| RA | 2,073,079 | T→C | L514P (CTG→CCG) | flu → | CP4‑44 prophage, antigen 43 (Ag43) phase‑variable biofilm formation autotransporter |
| 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 | 2,184,452 | G→A | A22V (GCC→GTC) | thiD ← | hydroxy‑methylpyrimidine kinase and hydroxy‑phosphomethylpyrimidine kinase |
| RA | 2,248,780 | C→T | R280Q (CGG→CAG) | yeiE ← | putative DNA‑binding transcriptional regulator |
| RA | 2,335,018 | G→A | L543L (CTG→TTG) | yfaA ← | DUF2138 family protein, putative host defense protein |
| RA | 2,366,245 | G→A | T106T (ACG→ACA) | arnB → | uridine 5'‑(beta‑1‑threo‑pentapyranosyl‑4‑ulose diphosphate) aminotransferase, PLP‑dependent |
| RA | 2,401,103 | G→A | T151T (ACC→ACT) | nuoF ← | NADH:ubiquinone oxidoreductase, chain F |
| RA | 2,481,904 | (A)8→9 | coding (273/1539 nt) | emrY ← | putative multidrug efflux system |
| RA | 2,484,916 | A→G | Q181Q (CAA→CAG) | evgS → | hybrid sensory histidine kinase in two‑component regulatory system with EvgA |
| RA | 2,562,984 | G→A | G154D (GGC→GAC) | yffP → | CPZ‑55 prophage, uncharacterized protein |
| RA | 2,691,927 | G→A | A1206V (GCG→GTG) | purL ← | phosphoribosylformyl‑glycineamide synthetase |
| RA | 2,763,869 | (T)7→8 | coding (1285/1617 nt) | yfjL ← | CP4‑57 putative defective prophage, DUF4297/DUF1837 polymorphic toxin family protein |
| RA | 2,765,794 | (C)7→8 | intergenic (‑18/‑124) | yfjM ← / → rnlA | CP4‑57 prophage, uncharacterized protein/CP4‑57 prophage, RNase LS |
| RA | 2,817,899 | T→C | intergenic (‑39/+160) | argQ ← / ← argZ | tRNA‑Arg/tRNA‑Arg |
| RA | 2,842,591 | T→C | L151L (TTA→TTG) | hycI ← | protease involved in processing C‑terminal end of HycE |
| RA | 2,913,461 | T→C | E64G (GAG→GGG) | relA ← | (p)ppGpp synthetase I/GTP pyrophosphokinase |
| RA | 2,937,802 | A→G | D112G (GAC→GGC) | fucK → | L‑fuculokinase |
| RA | 2,972,909 | (C)6→7 | coding (954/1194 nt) | lplT ← | lysophospholipid transporter |
| RA | 2,984,452 | (C)5→4 | coding (1141/1182 nt) | yqeF ← | short chain acyltransferase |
| RA | 3,055,285 | T→C | T54A (ACG→GCG) | ygfB ← | UPF0149 family protein |
| RA | 3,073,237 | T→C | N152S (AAC→AGC) | epd ← | D‑erythrose 4‑phosphate dehydrogenase |
| RA | 3,128,620 | A→G | T117A (ACG→GCG) | glcC → | glycolate‑inducible glc operon transcriptional repressor, autorepressor |
| RA | 3,139,583 | G→A | R286H (CGT→CAT) | yghU → | putative S‑transferase |
| RA | 3,271,600 | (C)5→6 | coding (171/1146 nt) | garK ← | glycerate kinase I |
| RA | 3,286,815 | T→C | H182H (CAT→CAC) | agaI → | galactosamine‑6‑phosphate isomerase |
| RA | 3,304,813 | (C)7→8 | coding (1005/1245 nt) | mtr ← | tryptophan transporter of high affinity |
| RA | 3,366,953 | G→A | G10R (GGA→AGA) | yhcF → | putative transcriptional regulator |
| RA | 3,457,094 | A→G | I240V (ATC→GTC) | gspD → | general secretory pathway component, cryptic |
| 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 | 3,791,004 | A→G | G114G (GGT→GGC) | tdh ← | L‑threonine 3‑dehydrogenase, NAD(P)‑binding |
| RA | 3,815,808 | (A)8→7 | intergenic (‑40/+26) | pyrE ← / ← rph | orotate phosphoribosyltransferase/ribonuclease PH (defective),enzyme, Degradation of RNA, RNase PH |
| RA | 3,880,017 | C→T | G35S (GGT→AGT) | gyrB ← | DNA gyrase, subunit B |
| RA | 3,901,765 | G→A | G152G (GGC→GGT) | bglH ← | carbohydrate‑specific outer membrane porin, cryptic |
| RA | 3,936,381 | C→T | T35M (ACG→ATG) | rbsB → | D‑ribose ABC transporter periplasmic binding protein, ribose chemotaxis receptor |
| RA | 4,188,171 | C→T | A941V (GCA→GTA) | rpoC → | RNA polymerase, beta prime subunit |
| RA | 4,188,572 | C→T | R1075C (CGT→TGT) | rpoC → | RNA polymerase, beta prime subunit |
| RA | 4,202,604 | C→T | R227C (CGC→TGC) | zraS → | sensory histidine kinase in two‑component regulatory system with ZraR |
| RA | 4,231,599 | C→T | M11I (ATG→ATA) | yjbD ← | DUF3811 family protein |
| RA | 4,281,472 | A→G | E498G (GAG→GGG) | yjcE → | putative cation/proton antiporter |
| RA | 4,296,381 | +GC | intergenic (+587/+55) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,351,093 | G→A | G190G (GGC→GGT) | dcuS ← | sensory histidine kinase in two‑component regulatory system with DcuR, regulator of anaerobic fumarate respiration |
| RA | 4,410,053 | (T)9→8 | intergenic (+47/‑80) | rlmB → / → yjfI | 23S rRNA mG2251 2'‑O‑ribose methyltransferase, SAM‑dependent/DUF2170 family protein |
| RA | 4,490,935 | A→G | L69L (TTG→CTG) | idnR ← | transcriptional repressor, 5‑gluconate‑binding |
| RA | 4,491,277 | T→C | T417A (ACG→GCG) | idnT ← | L‑idonate and D‑gluconate transporter |
| RA | 4,538,491 | C→T | G92D (GGC→GAC) | nanM ← | N‑acetylneuraminic acid mutarotase |
| RA | 4,548,789 | A→G | intergenic (+1/‑19) | fimG → / → fimH | minor component of type 1 fimbriae/minor component of type 1 fimbriae |
| RA | 4,574,259 | A→G | pseudogene (341/2937 nt) | yjiV → | pseudogene, conserved hypothetical protein |
| RA | 4,606,330 | (G)8→7 | noncoding (72/87 nt) | leuQ ← | tRNA‑Leu |
| RA | 4,614,343 | G→A | intergenic (+83/+337) | yjjV → / ← yjjW | putative DNase/putative pyruvate formate lyase activating enzyme |
| RA | 4,614,346 | T→C | intergenic (+86/+334) | yjjV → / ← yjjW | putative DNase/putative pyruvate formate lyase activating enzyme |
| RA | 4,614,422 | 2 bp→AA | intergenic (+162/+257) | yjjV → / ← yjjW | putative DNase/putative pyruvate formate lyase activating enzyme |
| RA | 4,636,673 | G→A | G223R (GGA→AGA) | creB → | response regulator in two‑component regulatory system with CreC |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 807347 | 810368 | 3022 | 4 [0] | [2] 8 | ybhB–[bioB] | ybhB, bioA, [bioB] |
| * | * | ÷ | NC_000913 | 1465202 | 1465233 | 32 | 4 [2] | [2] 3 | [ynbG] | [ynbG] |
| * | * | ÷ | NC_000913 | 2402310 | 2402335 | 26 | 4 [2] | [2] 3 | nuoC | NADH:ubiquinone oxidoreductase, fused CD subunit |
| * | * | ÷ | NC_000913 | 2857138 | 2859608 | 2471 | 3 [0] | [0] 5 | mutS | methyl‑directed mismatch repair protein |
| * | * | ÷ | NC_000913 | 3423796–3424234 | 3424523–3424242 | 9–728 | 3 [2] | [2] 5 | [rrlD] | [rrlD] |
| * | * | ÷ | NC_000913 | 4168387–4168471 | 4171522–4168573 | 103–3136 | 3 [2] | [2] 4 | [gltT]–[rrlB] | [gltT], [rrlB] |
| * | * | ÷ | NC_000913 | 4614383 | 4614403 | 21 | 3 [0] | [2] 4 | yjjV/yjjW | putative DNase/putative pyruvate formate lyase activating enzyme |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 1207790 = | 5 (0.170) | 41 (1.610) | 31/198 | 0.0 | 93.9% | coding (290/630 nt) | stfP | e14 prophage, uncharacterized protein |
| ? | NC_000913 | 1209619 = | 1 (0.040) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage, side tail fiber protein fragment family,Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 5 (0.170) | 12 (0.470) | 11/198 | 0.9 | 81.9% | coding (305/630 nt) | stfP | e14 prophage, uncharacterized protein |
| ? | NC_000913 | = 1209602 | 1 (0.040) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage, side tail fiber protein fragment family,Phage or Prophage Related | |||||