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 | 71,929 | G→A | W193* (TGG→TGA) | yabI → | DedA family inner membrane protein |
| MC JC | 257,908 | Δ776 bp | [crl] | [crl] | |
| MC | 279,931 | Δ11,471 bp | between IS1 | [insI1]–insA | [insI1], insX, yagB, yagA, yagE, yagF, yagG, yagH, yagI, argF, ykgS, insB1, insA |
| RA | 573,440 | C→T | R24C (CGC→TGC) | rusA → | DLP12 prophage, endonuclease RUS |
| RA | 580,905 | A→G | E24E (GAA→GAG) | nohD → | DLP12 prophage, DNA packaging protein |
| RA | 738,241 | T→C | F50F (TTT→TTC) | ybfD → | H repeat‑associated putative transposase |
| RA | 759,829 | C→T | A375V (GCG→GTG) | sucA → | 2‑oxoglutarate decarboxylase, thiamine triphosphate‑binding |
| RA | 865,008 | C→T | G41D (GGC→GAC) | moeB ← | molybdopterin synthase sulfurylase |
| 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 | 1,170,674 | C→T | P1097P (CCG→CCA) | mfd ← | transcription‑repair coupling factor |
| RA | 1,190,061 | (G)6→7 | coding (387/672 nt) | phoP ← | response regulator in two‑component regulatory system with PhoQ |
| RA | 1,212,012 | T→C | intergenic (‑9/+691) | iraM ← / ← ycgX | RpoS stabilzer during Mg starvation, anti‑RssB factor/DUF1398 family protein |
| RA | 1,241,732 | G→A | L114L (CTG→TTG) | cvrA ← | putative cation/proton antiporter |
| RA | 1,259,697 | C→T | P369P (CCG→CCA) | dauA ← | C4‑dicarboxylic acid transporter |
| RA | 1,278,189 | C→T | T78I (ACT→ATT) | narK → | nitrate/nitrite transporter |
| RA | 1,278,990 | G→A | G345D (GGC→GAC) | narK → | nitrate/nitrite transporter |
| RA | 1,287,826 | C→T | A267T (GCA→ACA) | purU ← | formyltetrahydrofolate hydrolase |
| 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→9 | pseudogene (3856/3861 nt) | yneO ← | pseudogene, AidA homolog |
| RA | 1,595,427 | A→G | pseudogene (2561/3861 nt) | yneO ← | pseudogene, AidA homolog |
| RA | 1,601,769 | G→A | E94K (GAA→AAA) | lsrA → | autoinducer 2 import ATP‑binding protein |
| RA | 1,766,416 | A→G | V757A (GTC→GCC) | ydiJ ← | putative FAD‑linked oxidoreductase |
| RA | 1,830,359 | T→C | N136S (AAC→AGC) | astA ← | arginine succinyltransferase |
| RA | 1,857,841 | T→C | S331S (TCA→TCG) | ydjJ ← | putative Zn‑dependent NAD(P)‑binding oxidoreductase |
| 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 | 1,977,418 | T→C | N143D (AAT→GAT) | flhC ← | flagellar class II regulon transcriptional activator, with FlhD |
| MC JC | 1,978,503 | Δ776 bp | insB1–insA | insB1, insA | |
| RA | 2,057,676 | (C)7→8 | intergenic (+102/+351) | yeeN → / ← asnW | UPF0082 family protein/tRNA‑Asn |
| 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 | 2,210,779 | G→A | pseudogene (1680/2001 nt) | yehQ → | pseudogene |
| RA | 2,223,735 | G→A | L517L (CTG→CTA) | dld → | D‑lactate dehydrogenase, FAD‑binding, NADH independent |
| RA | 2,248,780 | C→T | R280Q (CGG→CAG) | yeiE ← | putative DNA‑binding transcriptional regulator |
| RA | 2,305,466 | T→C | E430G (GAG→GGG) | mqo ← | malate dehydrogenase, FAD/NAD(P)‑binding domain |
| RA | 2,335,018 | G→A | L543L (CTG→TTG) | yfaA ← | DUF2138 family protein, putative host defense protein |
| RA | 2,380,360 | (C)5→6 | coding (284/1296 nt) | menF ← | isochorismate synthase 2 |
| RA | 2,401,103 | G→A | T151T (ACC→ACT) | nuoF ← | NADH:ubiquinone oxidoreductase, chain F |
| RA | 2,426,751 | G→A | A13V (GCC→GTC) | hisJ ← | histidine ABC transporter periplasmic binding protein |
| RA | 2,484,916 | A→G | Q181Q (CAA→CAG) | evgS → | hybrid sensory histidine kinase in two‑component regulatory system with EvgA |
| RA | 2,489,477 | T→C | K237R (AAG→AGG) | yfdV ← | putative transporter |
| JC | 2,602,017 | (C)7→10 | coding (200/2019 nt) | hyfB → | hydrogenase 4, membrane subunit |
| RA | 2,629,726 | A→G | intergenic (+245/‑66) | yfgG → / → yfgH | uncharacterized protein/outer membrane integrity lipoprotein |
| RA | 2,691,927 | G→A | A1206V (GCG→GTG) | purL ← | phosphoribosylformyl‑glycineamide synthetase |
| RA | 2,724,058 | C→T | D444D (GAC→GAT) | pssA → | phosphatidylserine synthase, CDP‑diacylglycerol‑serine O‑phosphatidyltransferase |
| 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 | 2,767,445 | (C)7→8 | intergenic (+90/‑265) | rnlB → / → yfjP | CP4‑57 prophage, uncharacterized protein/CP4‑57 prophage, 50S ribosome‑binding GTPase family protein |
| RA | 2,811,279 | G→A | V170V (GTG→GTA) | mprA → | transcriptional repressor of microcin B17 synthesis and multidrug efflux |
| RA | 2,842,591 | T→C | L151L (TTA→TTG) | hycI ← | protease involved in processing C‑terminal end of HycE |
| RA | 2,876,388 | C→T | intergenic (‑59/‑193) | cysD ← / → iap | sulfate adenylyltransferase, subunit 2/aminopeptidase in alkaline phosphatase isozyme conversion |
| RA | 2,937,802 | A→G | D112G (GAC→GGC) | fucK → | L‑fuculokinase |
| RA | 3,073,237 | T→C | N152S (AAC→AGC) | epd ← | D‑erythrose 4‑phosphate dehydrogenase |
| RA | 3,120,810 | G→A | A157V (GCG→GTG) | glcA ← | glycolate transporter |
| RA | 3,139,583 | G→A | R286H (CGT→CAT) | yghU → | putative S‑transferase |
| RA | 3,241,074 | C→T | G377G (GGC→GGT) | sstT → | sodium:serine/threonine symporter |
| 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 | 3,486,736 | T→C | V206A (GTT→GCT) | crp → | cAMP‑activated global transcription factor, mediator of catabolite repression |
| RA | 3,517,023 | G→A | A95V (GCC→GTC) | damX ← | cell division protein that binds to the septal ring |
| 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 | 3,580,930 | (A)9→8 | noncoding (87/90 nt) | ryhB ← | sRNA antisense regulator mediating positive Fur regulon response, Hfq‑dependent, global iron regulator |
| 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 | 3,823,683 | C→T | R428R (CGC→CGT) | spoT → | bifunctional (p)ppGpp synthetase II/ guanosine‑3',5'‑bis pyrophosphate 3'‑pyrophosphohydrolase |
| 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 | 3,950,476 | (T)8→9 | intergenic (+56/‑31) | ilvL → / → ilvX | ilvG operon leader peptide/uncharacterized protein |
| RA | 4,110,959 | T→C | A183A (GCA→GCG) | tpiA ← | triosephosphate isomerase |
| 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 | 4,293,106 | (G)7→8 | coding (1595/1659 nt) | nrfE → | heme lyase (NrfEFG) for insertion of heme into c552, subunit NrfE |
| RA | 4,296,381 | +GC | intergenic (+587/+55) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,305,268 | A→G | Y444H (TAT→CAT) | yjcS ← | metallo‑beta‑lactamase superfamily protein |
| RA | 4,347,002 | C→T | G109S (GGC→AGC) | fumB ← | anaerobic class I fumarate hydratase (fumarase B) |
| 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 | 4,409,911 | T→C | L213L (TTG→CTG) | rlmB → | 23S rRNA mG2251 2'‑O‑ribose methyltransferase, SAM‑dependent |
| RA | 4,479,980 | (T)7→8 | coding (251/1197 nt) | yjgN → | DUF898 family inner membrane 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 | 4,574,259 | A→G | pseudogene (341/2937 nt) | yjiV → | pseudogene, conserved hypothetical protein |
| RA | 4,635,299 | G→A | A4A (GCC→GCT) | rob ← | right oriC‑binding transcriptional activator, AraC family |
| 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 | 807331 | 810363 | 3033 | 11 [9] | [8] 11 | ybhB–[bioB] | ybhB, bioA, [bioB] |
| * | * | ÷ | NC_000913 | 2857138 | 2859626 | 2489 | 15 [0] | [10] 12 | mutS | methyl‑directed mismatch repair protein |
| * | * | ÷ | NC_000913 | 3423749–3424233 | 3424546–3424240 | 8–798 | 13 [10] | [10] 12 | [rrfD]–[rrlD] | [rrfD], [rrlD] |
| * | * | ÷ | NC_000913 | 3455424 | 3455478 | 55 | 17 [10] | [9] 12 | gspA/gspC | general secretory pathway component, cryptic/general secretory pathway component, cryptic |
| * | * | ÷ | NC_000913 | 4168365–4168559 | 4171544–4168573 | 15–3180 | 12 [10] | [7] 12 | gltT–[rrlB] | gltT, [rrlB] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 1207790 = | 3 (0.050) | 66 (1.400) | 42/188 | 0.1 | 95.3% | coding (290/630 nt) | stfP | e14 prophage, uncharacterized protein |
| ? | NC_000913 | 1209619 = | 4 (0.090) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage, side tail fiber protein fragment family,Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 3 (0.050) | 33 (0.700) | 27/188 | 0.5 | 91.0% | coding (305/630 nt) | stfP | e14 prophage, uncharacterized protein |
| ? | NC_000913 | = 1209602 | 4 (0.090) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage, side tail fiber protein fragment family,Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 67 (1.260) | 52/212 | 0.0 | 100% | intergenic (+253/‑1684) | ychE/oppA | UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein |
| ? | NC_000913 | 1300698 = | 0 (0.000) | intergenic (+1453/‑484) | ychE/oppA | UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein | |||||