mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.33.1 revision 8505477f25b3
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Predicted mutations | ||||||
|---|---|---|---|---|---|---|
| evidence | position | mutation | freq | annotation | gene | description |
| RA | 126,947 | G→T | 100% | R418L (CGT→CTT) | aceF → | pyruvate dehydrogenase, dihydrolipoyltransacetylase component E2 |
| RA | 180,794 | T→C | 6.8% | intergenic (+40/‑90) | dgt → / → degP | deoxyguanosine triphosphate triphosphohydrolase/serine endoprotease (protease Do), membrane‑associated |
| RA | 211,231 | T→A | 11.5% | L518H (CTC→CAC) | ldcC → | lysine decarboxylase 2, constitutive |
| RA | 256,449 | T→C | 7.2% | intergenic (+14/‑78) | gpt → / → frsA | xanthine phosphoribosyltransferase; xanthine‑guanine phosphoribosyltransferase/fermentation‑respiration switch protein; PTS Enzyme IIA(Glc)‑binding protein; pNP‑butyrate esterase activity |
| RA | 256,454 | C→G | 7.2% | intergenic (+19/‑73) | gpt → / → frsA | xanthine phosphoribosyltransferase; xanthine‑guanine phosphoribosyltransferase/fermentation‑respiration switch protein; PTS Enzyme IIA(Glc)‑binding protein; pNP‑butyrate esterase activity |
| RA | 256,459 | G→A | 7.4% | intergenic (+24/‑68) | gpt → / → frsA | xanthine phosphoribosyltransferase; xanthine‑guanine phosphoribosyltransferase/fermentation‑respiration switch protein; PTS Enzyme IIA(Glc)‑binding protein; pNP‑butyrate esterase activity |
| MC JC | 257,908 | Δ776 bp | 100% | [crl] | [crl] | |
| RA | 317,820 | A→G | 9.9% | L167P (CTG→CCG) | rclC ← | reactive chlorine species (RCS) stress resistance inner membrane protein |
| RA | 318,458 | G→A | 6.6% | S37L (TCA→TTA) | rclB ← | reactive chlorine species (RCS) stress resistance periplasmic protein |
| RA | 349,717 | T→C | 14.6% | intergenic (+145/‑295) | prpB → / → prpC | 2‑methylisocitrate lyase/2‑methylcitrate synthase |
| RA | 426,193 | T→C | 9.1% | F19F (TTT→TTC) | tgt → | tRNA‑guanine transglycosylase |
| RA | 435,390 | T→A | 11.4% | L85Q (CTG→CAG) | nusB → | transcription antitermination protein |
| RA | 435,396 | T→A | 11.2% | I87N (ATT→AAT) | nusB → | transcription antitermination protein |
| RA | 435,402 | T→A | 12.1% | L89Q (CTG→CAG) | nusB → | transcription antitermination protein |
| RA | 682,733 | C→T | 11.6% | A221T (GCC→ACC) | hscC ← | Hsp70 family chaperone Hsc62; RpoD‑binding transcription inhibitor |
| RA | 819,918 | A→G | 9.2% | Q12R (CAA→CGA) | ybhL → | putative acetate transporter; BAX Inhibitor‑1 family inner membrane protein |
| RA | 843,342 | A→T | 11.8% | V713V (GTT→GTA) | ybiO ← | mechanosensitive channel protein, intermediate conductance |
| RA | 843,347 | C→G | 12.9% | G712R (GGC→CGC) | ybiO ← | mechanosensitive channel protein, intermediate conductance |
| RA | 867,717 | G→C | 8.0% | L66F (TTG→TTC) | gsiA → | glutathione ABC transporter ATPase |
| RA | 867,718 | G→C | 8.0% | E67Q (GAA→CAA) | gsiA → | glutathione ABC transporter ATPase |
| RA | 952,625 | G→T | 8.7% | V310V (GTC→GTA) | pflB ← | formate C‑acetyltransferase 1, anaerobic; pyruvate formate‑lyase 1 |
| RA | 1,143,643 | T→G | 100% | Q242P (CAG→CCG) | rne ← | endoribonuclease; RNA‑binding protein;RNA degradosome binding protein |
| RA | 1,232,481 | C→T | 14.2% | intergenic (+27/+19) | umuC → / ← dsbB | translesion error‑prone DNA polymerase V subunit; DNA polymerase activity/oxidoreductase that catalyzes reoxidation of DsbA protein disulfide isomerase I |
| RA | 1,232,484 | A→G | 17.3% | intergenic (+30/+16) | umuC → / ← dsbB | translesion error‑prone DNA polymerase V subunit; DNA polymerase activity/oxidoreductase that catalyzes reoxidation of DsbA protein disulfide isomerase I |
| RA | 1,413,542 | A→T | 100% | Y67N (TAT→AAT) | ydaC ← | DUF1187 family protein, Rac prophage; putative double‑strand break reduction protein |
| RA | 1,793,897 | Δ1 bp | 100% | coding (213/552 nt) | btuE ← | glutathione peroxidase |
| RA | 1,865,682 | G→C | 11.2% | intergenic (‑46/+44) | yeaE ← / ← mipA | aldo‑keto reductase, methylglyoxal to acetol, NADPH‑dependent/scaffolding protein for murein synthesizing machinery |
| MC JC | 1,978,503 | Δ776 bp | 100% | insB1–insA | insB1, insA | |
| RA | 2,093,040 | G→A | 100% | A215T (GCT→ACT) | hisC → | histidinol‑phosphate aminotransferase |
| RA | 2,169,658 | C→A | 8.1% | intergenic (+47/+35) | yegS → / ← gatR | phosphatidylglycerol kinase, metal‑dependent/pseudogene, repressor for gat operon; interrupted by IS3; split galactitol utilization operon repressor, fragment 2; split galactitol utilization operon repressor, interrupted |
| RA | 2,169,664 | A→T | 8.2% | intergenic (+53/+29) | yegS → / ← gatR | phosphatidylglycerol kinase, metal‑dependent/pseudogene, repressor for gat operon; interrupted by IS3; split galactitol utilization operon repressor, fragment 2; split galactitol utilization operon repressor, interrupted |
| RA | 2,169,665 | A→T | 8.2% | intergenic (+54/+28) | yegS → / ← gatR | phosphatidylglycerol kinase, metal‑dependent/pseudogene, repressor for gat operon; interrupted by IS3; split galactitol utilization operon repressor, fragment 2; split galactitol utilization operon repressor, interrupted |
| RA | 2,169,671 | T→G | 7.8% | intergenic (+60/+22) | yegS → / ← gatR | phosphatidylglycerol kinase, metal‑dependent/pseudogene, repressor for gat operon; interrupted by IS3; split galactitol utilization operon repressor, fragment 2; split galactitol utilization operon repressor, interrupted |
| RA | 2,169,672 | T→C | 7.7% | intergenic (+61/+21) | yegS → / ← gatR | phosphatidylglycerol kinase, metal‑dependent/pseudogene, repressor for gat operon; interrupted by IS3; split galactitol utilization operon repressor, fragment 2; split galactitol utilization operon repressor, interrupted |
| RA | 2,202,356 | G→A | 11.1% | A694T (GCA→ACA) | yehI → | DUF4132 domain‑containing protein |
| RA | 2,429,943 | C→T | 7.1% | T98T (ACG→ACA) | purF ← | amidophosphoribosyltransferase |
| RA | 2,455,945 | T→C | 10.4% | intergenic (‑301/+380) | yfcV ← / ← sixA | putative fimbrial‑like adhesin protein/phosphohistidine phosphatase |
| RA | 2,486,807 | C→T | 9.9% | C812C (TGC→TGT) | evgS → | hybrid sensory histidine kinase in two‑component regulatory system with EvgA |
| RA | 2,767,665 | T→G | 9.0% | intergenic (+312/‑43) | rnlB → / → yfjP | CP4‑57 prophage; uncharacterized protein/CP4‑57 prophage; 50S ribosome‑binding GTPase family protein |
| RA | 2,767,668 | C→A | 8.9% | intergenic (+315/‑40) | rnlB → / → yfjP | CP4‑57 prophage; uncharacterized protein/CP4‑57 prophage; 50S ribosome‑binding GTPase family protein |
| RA | 2,972,650 | A→T | 6.8% | intergenic (+15/+17) | tas → / ← lplT | putative NADP(H)‑dependent aldo‑keto reductase/lysophospholipid transporter |
| RA | 2,972,651 | A→T | 6.7% | intergenic (+16/+16) | tas → / ← lplT | putative NADP(H)‑dependent aldo‑keto reductase/lysophospholipid transporter |
| RA | 3,078,184 | C→T | 9.2% | G225D (GGC→GAC) | cmtA ← | putative mannitol‑specific PTS IIB and IIC components |
| RA | 3,078,189 | A→G | 10.3% | G223G (GGT→GGC) | cmtA ← | putative mannitol‑specific PTS IIB and IIC components |
| RA | 3,183,282 | A→G | 7.6% | G245G (GGA→GGG) | zupT → | zinc transporter |
| RA | 3,345,224 | C→T | 8.4% | I170I (ATC→ATT) | rpoN → | RNA polymerase, sigma 54 (sigma N) factor |
| RA | 3,439,586 | G→C | 7.2% | intergenic (‑79/+28) | yhdN ← / ← rplQ | DUF1992 family protein/50S ribosomal subunit protein L17 |
| RA | 3,439,587 | G→C | 7.6% | intergenic (‑80/+27) | yhdN ← / ← rplQ | DUF1992 family protein/50S ribosomal subunit protein L17 |
| RA | 3,623,585 | A→G | 100% | E63G (GAA→GGA) | yhhH → | putative NTF2 fold immunity protein for polymorphic toxin RhsB |
| RA | 3,722,299 | G→T | 7.4% | intergenic (+195/+28) | sokA → / ← glyS | pseudogene, sRNA antisense regulator blocking mokA/hokA translation/glycine tRNA synthetase, beta subunit |
| RA | 3,722,300 | A→C | 7.3% | intergenic (+196/+27) | sokA → / ← glyS | pseudogene, sRNA antisense regulator blocking mokA/hokA translation/glycine tRNA synthetase, beta subunit |
| RA | 3,739,851 | T→C | 7.4% | F50L (TTC→CTC) | avtA → | valine‑pyruvate aminotransferase; transaminase C; alanine‑valine transaminase |
| RA | 3,877,557 | G→C | 8.1% | intergenic (‑93/+147) | yidB ← / ← gyrB | DUF937 family protein/DNA gyrase, subunit B |
| RA | 4,060,260 | G→T | 7.5% | intergenic (+31/‑186) | typA → / → yihL | GTP‑binding protein/putative DNA‑binding transcriptional regulator |
| RA | 4,116,703 | T→G | 100% | K173N (AAA→AAC) | glpK ← | glycerol kinase |
| RA | 4,127,250 | C→T | 7.9% | intergenic (+26/+35) | rpmE → / ← yiiX | 50S ribosomal subunit protein L31/putative lipid binding hydrolase, DUF830 family protein |
| RA | 4,127,251 | A→G | 7.6% | intergenic (+27/+34) | rpmE → / ← yiiX | 50S ribosomal subunit protein L31/putative lipid binding hydrolase, DUF830 family protein |
| RA | 4,150,903 | A→C | 8.7% | L732R (CTG→CGG) | ppc ← | phosphoenolpyruvate carboxylase |
| RA | 4,177,170 | T→A | 9.8% | intergenic (+43/‑187) | tufB → / → secE | translation elongation factor EF‑Tu 2/preprotein translocase membrane subunit |
| RA | 4,177,171 | T→A | 9.1% | intergenic (+44/‑186) | tufB → / → secE | translation elongation factor EF‑Tu 2/preprotein translocase membrane subunit |
| RA | 4,227,241 | T→A | 5.8% | Y1139N (TAT→AAT) | metH → | homocysteine‑N5‑methyltetrahydrofolate transmethylase, B12‑dependent |
| RA | 4,345,473 | A→G | 6.0% | H29H (CAT→CAC) | yjdF ← | DUF2238 family inner membrane protein |
| RA | 4,371,351 | C→T | 8.1% | A109V (GCG→GTG) | groL → | Cpn60 chaperonin GroEL, large subunit of GroESL |
| RA | 4,440,057 | A→G | 11.6% | M387T (ATG→ACG) | ytfL ← | UPF0053 family inner membrane protein |
| RA | 4,447,965 | T→A | 5.8% | L24* (TTA→TAA) | ytfP → | GGCT‑like protein |
| RA | 4,455,360 | G→A | 13.1% | A84V (GCG→GTG) | fbp ← | fructose‑1,6‑bisphosphatase I |
| RA | 4,569,910 | C→A | 7.7% | pseudogene (912/921 nt) | yjiP → | pseudogene, transposase_31 family protein |
| RA | 4,580,834 | T→C | 8.0% | T210T (ACA→ACG) | hsdS ← | specificity determinant for hsdM and hsdR |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 3423784–3424232 | 3424534–3424236 | 5–751 | 10 [9] | [9] 11 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 412077 = | 48 (1.070) | 3 (0.070) | 3/260 | NT | 6.3% | coding (405/1185 nt) | araJ | L‑arabinose‑inducible putative transporter, MFS family |
| ? | NC_000913 | 412119 = | 44 (1.040) | coding (363/1185 nt) | araJ | L‑arabinose‑inducible putative transporter, MFS family | |||||
| * | ? | NC_000913 | = 998212 | 37 (0.820) | 3 (0.070) | 3/264 | NT | 7.8% | coding (345/540 nt) | elfA | laminin‑binding fimbrin subunit |
| ? | NC_000913 | = 998309 | 36 (0.840) | coding (442/540 nt) | elfA | laminin‑binding fimbrin subunit | |||||
| * | ? | NC_000913 | 1048957 = | 39 (0.870) | 3 (0.070) | 3/268 | NT | 8.2% | coding (376/645 nt) | gfcB | O‑antigen capsule production lipoprotein |
| ? | NC_000913 | 1048998 = | 29 (0.660) | coding (335/645 nt) | gfcB | O‑antigen capsule production lipoprotein | |||||
| * | ? | NC_000913 | 1207790 = | 16 (0.360) | 12 (0.300) | 8/244 | NT | 42.8% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | 1209619 = | 18 (0.450) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 15 (0.330) | 11 (0.280) | 11/244 | NT | 41.3% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | = 1209602 | 18 (0.450) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 30 (0.690) | 25/268 | NT | 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 | |||||
| * | ? | NC_000913 | 1396531 = | NA (NA) | 4 (0.090) | 3/264 | NT | NA | coding (456/1017 nt) | insH1 | IS5 transposase and trans‑activator |
| ? | NC_000913 | = 1428264 | NA (NA) | coding (463/981 nt) | insH1 | IS5 transposase and trans‑activator | |||||
| * | ? | NC_000913 | = 1469240 | NA (NA) | 42 (0.930) | 31/276 | NT | 100% | intergenic (‑91/‑1) | insC1/ydbA | IS2 repressor TnpA/pseudogene, autotransporter homolog; interrupted by IS2 and IS30 |
| ? | NC_000913 | = 1652258 | 0 (0.000) | pseudogene (708/1158 nt) | intQ | pseudogene, Qin prophage; phage integrase family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1651547 | NA (NA) | 53 (1.190) | 38/274 | NT | 100% | intergenic (+10/‑4) | insD1/intQ | IS2 transposase TnpB;IS, phage, Tn; Transposon‑related functions; extrachromosomal; transposon related/pseudogene, Qin prophage; phage integrase family;Phage or Prophage Related |
| ? | NC_000913 | 1652253 = | 0 (0.000) | pseudogene (703/1158 nt) | intQ | pseudogene, Qin prophage; phage integrase family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | 1997426 = | 36 (0.800) | 5 (0.110) | 3/268 | NT | 13.0% | coding (389/753 nt) | yecC | putative ABC transporter ATPase |
| ? | NC_000913 | 1997455 = | 32 (0.730) | coding (360/753 nt) | yecC | putative ABC transporter ATPase | |||||
| * | ? | NC_000913 | 2406857 = | 0 (0.000) | 38 (0.850) | 32/274 | NT | 100% | intergenic (‑218/‑702) | lrhA/alaA | transcriptional repressor of flagellar, motility and chemotaxis genes/glutamate‑pyruvate aminotransferase; glutamic‑pyruvic transaminase (GPT); alanine transaminase |
| ? | NC_000913 | = 2997688 | NA (NA) | intergenic (‑90/+2) | insC1/ygeQ | IS2 repressor TnpA/pseudogene, glycosyl hydrolase family 15, part of T3SS PAI ETT2 remnant | |||||
| * | ? | NC_000913 | = 2406863 | 2 (0.040) | 46 (1.030) | 37/274 | NT | 95.9% | intergenic (‑224/‑696) | lrhA/alaA | transcriptional repressor of flagellar, motility and chemotaxis genes/glutamate‑pyruvate aminotransferase; glutamic‑pyruvic transaminase (GPT); alanine transaminase |
| ? | NC_000913 | 2996360 = | NA (NA) | intergenic (‑2/+10) | ygeO/insD1 | pseudogene, orgA family, part of T3SS PAI ETT2 remnant/IS2 transposase TnpB | |||||
| * | ? | NC_000913 | 2418607 = | 49 (1.090) | 3 (0.080) | 3/232 | NT | 6.5% | intergenic (+8/+25) | yfcC/yfcD | putative inner membrane transporter; C4‑dicarboxylate anaerobic carrier family protein/putative NUDIX hydrolase |
| ? | NC_000913 | 2418629 = | 45 (1.190) | intergenic (+30/+3) | yfcC/yfcD | putative inner membrane transporter; C4‑dicarboxylate anaerobic carrier family protein/putative NUDIX hydrolase | |||||
| * | ? | NC_000913 | 2432323 = | 35 (0.780) | 4 (0.090) | 4/264 | NT | 11.2% | coding (618/1269 nt) | folC | bifunctional folylpolyglutamate synthase/ dihydrofolate synthase |
| ? | NC_000913 | 2432375 = | 30 (0.700) | coding (566/1269 nt) | folC | bifunctional folylpolyglutamate synthase/ dihydrofolate synthase | |||||
| * | ? | NC_000913 | = 2646139 | 50 (1.110) | 3 (0.070) | 3/264 | NT | 6.0% | coding (1185/2313 nt) | pbpC | penicillin‑insensitive murein repair transglycosylase; inactive transpeptidase domain protein |
| ? | NC_000913 | = 2646150 | 46 (1.070) | coding (1174/2313 nt) | pbpC | penicillin‑insensitive murein repair transglycosylase; inactive transpeptidase domain protein | |||||
| * | ? | NC_000913 | = 2850291 | 58 (1.290) | 3 (0.070) | 3/264 | NT | 5.5% | coding (143/462 nt) | hycA | regulator of the transcriptional regulator FhlA |
| ? | NC_000913 | = 2850310 | 47 (1.090) | coding (124/462 nt) | hycA | regulator of the transcriptional regulator FhlA | |||||
| * | ? | NC_000913 | 3186094 = | NA (NA) | 57 (1.270) | 40/276 | NT | 100% | intergenic (+6/‑91) | yqiG/insC1 | pseudogene; fimbrial export usher family;putative membrane; Not classified; putative membrane protein/IS2 repressor TnpA |
| ? | NC_000913 | 3485933 = | 0 (0.000) | intergenic (‑117/‑185) | yhfA/crp | OsmC family protein/cAMP‑activated global transcription factor, mediator of catabolite repression | |||||
| * | ? | NC_000913 | = 3187424 | NA (NA) | 39 (0.870) | 30/276 | NT | 100% | intergenic (+11/‑1) | insD1/yqiG | IS2 transposase TnpB/pseudogene; fimbrial export usher family;putative membrane; Not classified; putative membrane protein |
| ? | NC_000913 | = 3485937 | 0 (0.000) | intergenic (‑121/‑181) | yhfA/crp | OsmC family protein/cAMP‑activated global transcription factor, mediator of catabolite repression | |||||
| * | ? | NC_000913 | 3296197 = | 56 (1.250) | 3 (0.070) | 3/260 | NT | 6.0% | coding (391/591 nt) | diaA | DnaA initiator‑associating factor for replication initiation |
| ? | NC_000913 | 3296251 = | 41 (0.970) | coding (445/591 nt) | diaA | DnaA initiator‑associating factor for replication initiation | |||||
| * | ? | NC_000913 | = 3534494 | 47 (1.050) | 3 (0.070) | 3/254 | NT | 6.4% | intergenic (+56/+20) | pck/envZ | phosphoenolpyruvate carboxykinase [ATP]/sensory histidine kinase in two‑component regulatory system with OmpR |
| ? | NC_000913 | = 3534500 | 45 (1.090) | intergenic (+62/+14) | pck/envZ | phosphoenolpyruvate carboxykinase [ATP]/sensory histidine kinase in two‑component regulatory system with OmpR | |||||
| * | ? | NC_000913 | = 3884920 | 44 (0.980) | 5 (0.120) | 4/258 | NT | 9.6% | coding (106/258 nt) | yidD | membrane protein insertion efficiency factor, UPF0161 family inner membrane protein |
| ? | NC_000913 | = 3884956 | 53 (1.260) | coding (142/258 nt) | yidD | membrane protein insertion efficiency factor, UPF0161 family inner membrane protein | |||||
| * | ? | NC_000913 | 4112782 = | 47 (1.050) | 4 (0.100) | 3/258 | NT | 8.3% | intergenic (+28/‑184) | yiiR/yiiS | DUF805 family putative inner membrane protein/UPF0381 family protein |
| ? | NC_000913 | 4112830 = | 44 (1.050) | intergenic (+76/‑136) | yiiR/yiiS | DUF805 family putative inner membrane protein/UPF0381 family protein | |||||