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 | 310 | (T)9→8 | intergenic (+55/‑27) | thrL → / → thrA | thr operon leader peptide/Bifunctional aspartokinase/homoserine dehydrogenase 1 |
| RA | 61,437 | C→T | V610M (GTG→ATG) | rapA ← | RNA polymerase remodeling/recycling factor ATPase, RNA polymerase‑associated, ATP‑dependent RNA translocase |
| RA | 92,846 | C→T | G478G (GGC→GGT) | ftsI → | transpeptidase involved in septal peptidoglycan synthesis, penicillin‑binding protein 3 |
| MC JC | 257,908 | Δ776 bp | [crl] | [crl] | |
| RA | 281,050 | (G)5→6 | coding (934/1155 nt) | yagA ← | CP4‑6 prophage, putative DNA‑binding transcriptional regulator |
| RA | 337,217 | T→C | V147A (GTC→GCC) | yahF → | putative NAD(P)‑binding succinyl‑CoA synthase |
| RA | 398,108 | G→A | V79V (GTG→GTA) | yaiW → | microcin Bac7 uptake protein, outer membrane surface‑exposed lipoprotein |
| RA | 573,440 | C→T | R24C (CGC→TGC) | rusA → | DLP12 prophage, endonuclease RUS |
| RA | 663,640 | A→G | G108G (GGT→GGC) | dacA ← | D‑alanyl‑D‑alanine carboxypeptidase (penicillin‑binding protein 5) |
| RA | 776,722 | C→T | A127A (GCC→GCT) | tolA → | membrane anchored protein in TolA‑TolQ‑TolR complex |
| RA | 924,093 | A→G | D277G (GAC→GGC) | clpA → | ATPase and specificity subunit of ClpA‑ClpP ATP‑dependent serine protease, chaperone activity |
| RA | 986,267 | C→T | G239D (GGT→GAT) | ompF ← | outer membrane porin 1a (Ia,b,F) |
| RA | 1,097,144 | (C)6→7 | intergenic (+315/+421) | ycdU → / ← serX | putative inner membrane protein/tRNA‑Ser |
| RA | 1,121,934 | A→G | I225T (ATC→ACC) | pyrC ← | dihydro‑orotase |
| RA | 1,190,061 | (G)6→7 | coding (387/672 nt) | phoP ← | response regulator in two‑component regulatory system with PhoQ |
| RA | 1,212,088 | (C)8→9 | intergenic (‑85/+615) | iraM ← / ← ycgX | RpoS stabilzer during Mg starvation, anti‑RssB factor/DUF1398 family 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 | 1,458,617 | A→G | A118A (GCA→GCG) | paaG → | 1,2‑epoxyphenylacetyl‑CoA isomerase, oxepin‑CoA‑forming |
| RA | 1,595,427 | A→G | pseudogene (2561/3861 nt) | yneO ← | pseudogene, AidA homolog |
| RA | 1,656,658 | G→A | A159T (GCC→ACC) | speG → | spermidine N(1)‑acetyltransferase |
| RA | 1,661,308 | T→C | R251R (CGT→CGC) | ynfF → | S‑ and N‑oxide reductase, A subunit, periplasmic |
| RA | 1,757,108 | T→C | *471Q (TAA→CAA) | pykF → | pyruvate kinase I |
| RA | 1,904,586 | T→C | V231A (GTC→GCC) | manZ → | mannose‑specific enzyme IID component of PTS |
| RA | 1,934,968 | T→C | V449V (GTA→GTG) | zwf ← | glucose‑6‑phosphate 1‑dehydrogenase |
| RA | 1,967,135 | (C)5→6 | coding (303/390 nt) | cheY ← | chemotaxis regulator transmitting signal to flagellar motor component |
| MC JC | 1,978,503 | Δ776 bp | insB1–insA | insB1, insA | |
| RA | 2,073,094 | T→C | L519P (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 | 2,248,780 | C→T | R280Q (CGG→CAG) | yeiE ← | putative DNA‑binding transcriptional regulator |
| RA | 2,288,561 | (C)7→6 | pseudogene (354/2525 nt) | yejO ← | pseudogene, autotransporter outer membrane homology,putative transport, Not classified, putative ATP‑binding component of a transport system |
| RA | 2,306,934 | A→G | intergenic (‑180/+38) | mqo ← / ← yojI | malate dehydrogenase, FAD/NAD(P)‑binding domain/microcin J25 efflux ABC transporter permease/ATPase |
| RA | 2,401,103 | G→A | T151T (ACC→ACT) | nuoF ← | NADH:ubiquinone oxidoreductase, chain F |
| RA | 2,482,862 | A→G | L160L (TTA→CTA) | emrK ← | multidrug resistance efflux pump membrane fusion protein |
| RA | 2,597,778 | A→G | intergenic (‑160/+53) | purC ← / ← bamC | phosphoribosylaminoimidazole‑succinocarboxamide synthetase/BamABCDE complex OM biogenesis lipoprotein |
| RA | 2,634,449 | G→A | R73H (CGC→CAC) | xseA → | exonuclease VII, large subunit |
| RA | 2,672,123 | G→A | G26E (GGG→GAG) | hcaD → | phenylpropionate dioxygenase, ferredoxin reductase subunit |
| RA | 2,734,543 | (C)8→9 | coding (492/732 nt) | yfiH ← | UPF0124 family protein |
| RA | 2,763,869 | (T)7→8 | coding (1285/1617 nt) | yfjL ← | CP4‑57 putative defective prophage, DUF4297/DUF1837 polymorphic toxin family protein |
| RA | 2,842,591 | T→C | L151L (TTA→TTG) | hycI ← | protease involved in processing C‑terminal end of HycE |
| RA | 2,899,230 | T→C | V63V (GTA→GTG) | ygcU ← | putative FAD‑linked oxidoreductase |
| RA | 2,916,189 | T→C | L378P (CTG→CCG) | barA → | hybrid sensory histidine kinase, in two‑component regulatory system with UvrY |
| RA | 2,931,839 | T→C | intergenic (+29/+26) | ygdG → / ← fucO | Ssb‑binding protein, misidentified as ExoIX/L‑1,2‑propanediol oxidoreductase |
| RA | 2,937,802 | A→G | D112G (GAC→GGC) | fucK → | L‑fuculokinase |
| RA | 3,068,541 | T→C | T90A (ACA→GCA) | argO ← | arginine transporter |
| RA | 3,081,402 | G→A | T78T (ACC→ACT) | tktA ← | transketolase 1, thiamine triphosphate‑binding |
| RA | 3,097,854 | G→A | L196L (CTG→CTA) | yggW → | HemN family putative oxidoreductase |
| RA | 3,139,583 | G→A | R286H (CGT→CAT) | yghU → | putative S‑transferase |
| RA | 3,189,993 | A→G | E38G (GAG→GGG) | yqiH → | putative periplasmic pilin chaperone |
| RA | 3,216,824 | C→T | R16C (CGC→TGC) | yqjI → | PadR family putative transcriptional regulator |
| RA | 3,256,048 | G→A | R202C (CGC→TGC) | yhaM ← | putative L‑serine dehydratase alpha chain |
| RA | 3,271,600 | (C)5→6 | coding (171/1146 nt) | garK ← | glycerate kinase I |
| RA | 3,304,813 | (C)7→8 | coding (1005/1245 nt) | mtr ← | tryptophan transporter of high affinity |
| RA | 3,304,862 | G→A | A319V (GCT→GTT) | mtr ← | tryptophan transporter of high affinity |
| RA | 3,344,045 | G→A | L34L (CTG→CTA) | lptB → | lipopolysaccharide export ABC transporter ATPase |
| RA | 3,347,929 | T→C | V272A (GTC→GCC) | yhbJ → | adaptor protein for GlmZ/GlmY sRNA decay, glucosamine‑6‑phosphate‑regulated, NTPase |
| RA | 3,366,953 | G→A | G10R (GGA→AGA) | yhcF → | putative transcriptional regulator |
| RA | 3,440,918 | T→C | T38A (ACT→GCT) | rpoA ← | RNA polymerase, alpha subunit |
| RA | 3,450,674 | G→A | P231S (CCA→TCA) | rplB ← | 50S ribosomal subunit protein L2 |
| RA | 3,456,838 | T→C | G154G (GGT→GGC) | gspD → | general secretory pathway component, cryptic |
| RA | 3,457,094 | A→G | I240V (ATC→GTC) | gspD → | general secretory pathway component, cryptic |
| RA | 3,485,541 | C→T | G93D (GGT→GAT) | yhfA ← | OsmC family protein |
| 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 | 3,607,418 | C→T | A323V (GCC→GTC) | zntA → | zinc, cobalt and lead efflux system |
| RA | 3,791,004 | A→G | G114G (GGT→GGC) | tdh ← | L‑threonine 3‑dehydrogenase, NAD(P)‑binding |
| RA | 3,815,811 | C→T | intergenic (‑43/+23) | pyrE ← / ← rph | orotate phosphoribosyltransferase/ribonuclease PH (defective),enzyme, Degradation of RNA, RNase PH |
| RA | 3,901,765 | G→A | G152G (GGC→GGT) | bglH ← | carbohydrate‑specific outer membrane porin, cryptic |
| RA | 3,901,992 | C→T | A77T (GCC→ACC) | bglH ← | carbohydrate‑specific outer membrane porin, cryptic |
| RA | 3,918,745 | A→G | G371G (GGT→GGC) | atpA ← | F1 sector of membrane‑bound ATP synthase, alpha subunit |
| RA | 3,936,381 | C→T | T35M (ACG→ATG) | rbsB → | D‑ribose ABC transporter periplasmic binding protein, ribose chemotaxis receptor |
| RA | 4,186,292 | G→A | A315T (GCG→ACG) | rpoC → | RNA polymerase, beta prime subunit |
| RA | 4,251,860 | (T)7→6 | pseudogene (900/1323 nt) | yjbI → | pseudogene, SopA‑related, pentapeptide repeats‑containing |
| RA | 4,266,510 | C→T | A243A (GCC→GCT) | alr → | alanine racemase, biosynthetic, PLP‑binding |
| 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 | 4,361,357 | A→G | L193S (TTG→TCG) | cadC ← | cadBA operon transcriptional activator |
| RA | 4,490,935 | A→G | L69L (TTG→CTG) | idnR ← | transcriptional repressor, 5‑gluconate‑binding |
| 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 | 4,575,425 | A→G | pseudogene (1507/2937 nt) | yjiV → | pseudogene, conserved hypothetical protein |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 271489–271585 | 271642–271590 | 6–154 | 3 [2] | [2] 3 | insI1 | IS30 transposase |
| * | * | ÷ | NC_000913 | 807347 | 810361 | 3015 | 3 [0] | [2] 4 | ybhB–[bioB] | ybhB, bioA, [bioB] |
| * | * | ÷ | NC_000913 | 1465200 | 1465226 | 27 | 3 [2] | [2] 4 | ynbG | uncharacterized protein |
| * | * | ÷ | NC_000913 | 2857138 | 2859608 | 2471 | 7 [0] | [0] 3 | mutS | methyl‑directed mismatch repair protein |
| * | * | ÷ | NC_000913 | 3423784–3424233 | 3424522–3424242 | 10–739 | 3 [2] | [1] 3 | [rrfD]–[rrlD] | [rrfD], [rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 381258 = | NA (NA) | 6 (0.200) | 3/224 | 2.8 | NA | pseudogene (3/417 nt) | yaiX | pseudogene, interrupted by IS2A, hexapeptide transferase superfamily, putative transferase |
| ? | NC_000913 | = 382589 | NA (NA) | noncoding (1330/1331 nt) | IS2 | repeat region | |||||
| * | ? | NC_000913 | 1207790 = | 5 (0.170) | 21 (0.810) | 19/194 | 0.3 | 87.0% | coding (290/630 nt) | stfP | e14 prophage, uncharacterized protein |
| ? | NC_000913 | 1209619 = | 2 (0.080) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage, side tail fiber protein fragment family,Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 5 (0.170) | 19 (0.730) | 17/194 | 0.4 | 85.8% | coding (305/630 nt) | stfP | e14 prophage, uncharacterized protein |
| ? | NC_000913 | = 1209602 | 2 (0.080) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage, side tail fiber protein fragment family,Phage or Prophage Related | |||||