mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.35.4 revision f352f80f4bc9
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Predicted mutations | ||||||
|---|---|---|---|---|---|---|
| evidence | position | mutation | freq | annotation | gene | description |
| RA | 68,880 | T→G | 13.9% | H390P (CAC→CCC) | araB ← | L‑ribulokinase |
| RA | 74,046 | A→G | 18.0% | L159P (CTC→CCC) | thiP ← | thiamine/thiamine pyrophosphate ABC transporter permease |
| MC JC | 257,908 | Δ776 bp | 100% | [crl] | [crl] | |
| RA | 303,404 | A→T | 11.3% | L138F (TTA→TTT) | yagU → | DUF1440 family inner membrane acid resistance protein |
| JC JC | 458,790 | IS186 (–) +6 bp :: Δ1 bp | 81.2% | intergenic (+90/‑93) | clpX → / → lon | ATPase and specificity subunit of ClpX‑ClpP ATP‑dependent serine protease/DNA‑binding ATP‑dependent protease La |
| RA | 494,160 | G→C | 6.0% | A29P (GCG→CCG) | ybaB → | DNA‑binding protein, putative nucleoid‑associated protein |
| RA | 647,210 | A→C | 21.2% | G100G (GGT→GGG) | citG ← | 2‑(5''‑triphosphoribosyl)‑3'‑dephosphocoenzyme‑A synthase |
| RA | 653,049 | T→G | 21.5% | V272G (GTG→GGG) | citA → | sensory histidine kinase in two‑component regulatory system with CitB |
| RA | 665,104 | A→C | 10.2% | S29R (AGT→AGG) | rlpA ← | septal ring protein, suppressor of prc, minor lipoprotein |
| RA | 673,888 | T→C | 14.6% | E299G (GAG→GGG) | leuS ← | leucyl‑tRNA synthetase |
| RA | 734,765 | T→G | 25.9% | pseudogene (633/1521 nt) | rhsO → | pseudogene, Rhs family |
| RA | 734,789 | T→G | 23.4% | pseudogene (657/1521 nt) | rhsO → | pseudogene, Rhs family |
| RA | 734,952 | T→G | 14.3% | pseudogene (820/1521 nt) | rhsO → | pseudogene, Rhs family |
| RA | 807,112 | T→G | 26.1% | H57P (CAC→CCC) | ybhC ← | acyl‑CoA thioesterase, lipoprotein |
| RA | 921,692 | T→G | 12.6% | V449G (GTG→GGG) | macB → | macrolide ABC transporter peremase/ATPase |
| RA | 956,640 | A→C | 12.9% | intergenic (‑8/‑122) | ycaO ← / → ycaP | ribosomal protein S12 methylthiotransferase accessory factor/UPF0702 family putative inner membrane protein |
| RA | 983,900 | A→G | 12.6% | E84G (GAG→GGG) | ycbL → | putative metal‑binding enzyme |
| RA | 1,058,486 | T→C | 14.5% | S135P (TCG→CCG) | torC → | trimethylamine N‑oxide (TMAO) reductase I, cytochrome c‑type subunit |
| RA | 1,065,745 | A→G | 12.5% | E54G (GAG→GGG) | agp → | glucose‑1‑phosphatase/inositol phosphatase |
| RA | 1,130,055 | A→T | 16.8% | V25E (GTA→GAA) | flgM ← | anti‑sigma factor for FliA (sigma 28) |
| RA | 1,170,684 | T→G | 14.1% | H1094P (CAC→CCC) | mfd ← | transcription‑repair coupling factor |
| RA | 1,175,770 | T→C | 12.7% | L115P (CTC→CCC) | lolC → | lipoprotein‑releasing system transmembrane protein |
| RA | 1,196,305 | C→T | 79.2% | R395C (CGT→TGT) | icd → | isocitrate dehydrogenase; e14 prophage attachment site; tellurite reductase |
| RA | 1,242,879 | T→G | 16.1% | T68P (ACC→CCC) | ldcA ← | murein tetrapeptide carboxypeptidase; LD‑carboxypeptidase A |
| JC JC | 1,293,032 | IS1 (–) +8 bp | 100% | intergenic (‑110/‑488) | hns ← / → tdk | global DNA‑binding transcriptional dual regulator H‑NS/thymidine kinase/deoxyuridine kinase |
| MC JC | 1,299,499 | Δ1,199 bp | 100% | intergenic (+254/‑485) | ychE → / → oppA | UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein |
| RA | 1,331,043 | T→G | 9.5% | intergenic (‑375/‑5) | yciN ← / → topA | DUF2498 protein YciN/DNA topoisomerase I, omega subunit |
| RA | 1,365,746 | A→G | 13.7% | E66G (GAG→GGG) | puuE → | 4‑aminobutyrate aminotransferase, PLP‑dependent |
| RA | 1,415,401 | A→T | 13.0% | S662R (AGT→AGA) | recE ← | Rac prophage; exonuclease VIII, 5' to 3' specific dsDNA exonuclease |
| RA | 1,435,706 | T→A | 13.0% | intergenic (‑87/+54) | uspF ← / ← ompN | stress‑induced protein, ATP‑binding protein/outer membrane pore protein N, non‑specific |
| RA | 1,720,129 | C→T | 13.4% | S85F (TCT→TTT) | slyB → | outer membrane lipoprotein |
| RA | 1,825,164 | A→T | 27.0% | G154G (GGT→GGA) | spy ← | periplasmic ATP‑independent protein refolding chaperone, stress‑induced |
| MC JC | 1,978,503 | Δ776 bp | 100% | insB1–insA | insB1, insA | |
| JC JC | 1,979,486 | IS5 (+) +4 bp | 100% | intergenic (‑271/‑264) | insA ← / → uspC | IS1 repressor TnpA/universal stress protein |
| RA | 2,014,217 | C→A | 22.0% | A330E (GCA→GAA) | fliF → | flagellar basal‑body MS‑ring and collar protein |
| RA | 2,080,362 | A→C | 16.1% | V77G (GTG→GGG) | yeeA ← | putative transporter, FUSC family inner membrane protein |
| RA | 2,120,818 | A→G | 21.1% | L246P (CTC→CCC) | wcaJ ← | colanic biosynthesis UDP‑glucose lipid carrier transferase |
| RA | 2,126,971 | T→G | 13.6% | T74P (ACC→CCC) | wcaG ← | bifunctional GDP‑fucose synthetase: GDP‑4‑dehydro‑6‑deoxy‑D‑mannose epimerase/ GDP‑4‑dehydro‑6‑L‑deoxygalactose reductase |
| RA | 2,132,787 | A→C | 100% | I204S (ATC→AGC) | wcaA ← | putative glycosyl transferase |
| RA | 2,145,868 | A→G | 16.2% | E868G (GAG→GGG) | yegE → | putative diguanylate cyclase |
| RA | 2,173,361 | Δ2 bp | 100% | pseudogene (1‑2/442 nt) | gatC ← | pseudogene, galactitol‑specific enzyme IIC component of PTS;transport; Transport of small molecules: Carbohydrates, organic acids, alcohols; PTS system galactitol‑specific enzyme IIC |
| RA | 2,195,582 | T→G | 13.8% | V428G (GTG→GGG) | metG → | methionyl‑tRNA synthetase |
| RA | 2,424,823 | T→C | 9.3% | R137R (AGA→AGG) | hisM ← | histidine ABC transporter permease |
| RA | 2,477,259 | T→G | 19.2% | D124A (GAC→GCC) | dsdC ← | dsd operon activator; autorepressor |
| JC JC | 2,536,312 | Δ1 bp :: IS186 (+) +6 bp :: Δ1 bp | 19.1% | coding (479‑484/510 nt) | crr → | glucose‑specific enzyme IIA component of PTS |
| RA | 2,718,259 | A→C | 12.3% | S90R (AGT→AGG) | yfiF ← | putative methyltransferase |
| RA | 2,776,555 | A→G | 10.6% | E57G (GAG→GGG) | yfjY → | CP4‑57 prophage; putative DNA repair protein |
| RA | 2,876,559 | G→T | 19.2% | intergenic (‑230/‑22) | cysD ← / → iap | sulfate adenylyltransferase, subunit 2/aminopeptidase in alkaline phosphatase isozyme conversion |
| RA | 2,877,027 | T→G | 15.6% | G149G (GGT→GGG) | iap → | aminopeptidase in alkaline phosphatase isozyme conversion |
| RA | 2,903,069 | G→T | 13.6% | A392S (GCC→TCC) | ygcE → | putative kinase |
| RA | 2,978,166 | T→A | 21.0% | Y245F (TAT→TTT) | lysA ← | diaminopimelate decarboxylase, PLP‑binding |
| RA | 3,027,731 | A→G | 13.0% | E204G (GAG→GGG) | ghxQ → | guanine/hypoxanthine permease, high affinity; guanine/hypoxanthine:H+ symporter |
| RA | 3,124,053 | T→C | 14.3% | E60G (GAG→GGG) | glcG ← | DUF336 family protein |
| RA | 3,178,958 | T→C | 12.5% | S282P (TCT→CCT) | tolC → | transport channel |
| RA | 3,277,509 | A→G | 14.6% | E58G (GAG→GGG) | yhaV → | toxin of the SohB(PrlF)‑YhaV toxin‑antitoxin system |
| RA | 3,293,719 | A→G | 17.8% | E107G (GAG→GGG) | lpoA → | OM lipoprotein stimulator of MrcA transpeptidase |
| RA | 3,313,745 | A→C | 10.8% | V757G (GTG→GGG) | infB ← | translation initiation factor IF‑2 |
| RA | 3,335,760 | A→G | 14.0% | S245S (TCT→TCC) | murA ← | UDP‑N‑acetylglucosamine 1‑carboxyvinyltransferase |
| RA | 3,412,898 | C→T | 11.4% | A190T (GCC→ACC) | acrS ← | acrAB operon transcriptional repressor |
| RA | 3,521,057 | A→C | 16.7% | G131G (GGT→GGG) | hofO ← | DNA catabolic protein |
| RA | 3,532,595 | C→A | 16.7% | intergenic (‑156/‑223) | yhgE ← / → pck | DUF4153 family putative inner membrane protein/phosphoenolpyruvate carboxykinase [ATP] |
| RA | 3,560,455:1 | +G | 100% | 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 | 3,608,249 | A→G | 17.0% | E600G (GAG→GGG) | zntA → | zinc, cobalt and lead efflux system |
| RA | 3,670,360 | A→G | 5.4% | M257V (ATG→GTG) | treF → | cytoplasmic trehalase |
| RA | 3,749,743 | A→G | 18.2% | E171G (GAG→GGG) | sgbU → | putative L‑xylulose 5‑phosphate 3‑epimerase |
| RA | 3,782,913 | A→C | 37.8% | V250G (GTG→GGG) | gpsA ← | glycerol‑3‑phosphate dehydrogenase (NAD+) |
| MC JC | 3,815,859 | Δ82 bp | 100% | [rph]–[rph] | [rph], [rph] | |
| RA | 3,817,477 | T→C | 9.6% | S268P (TCC→CCC) | yicC → | UPF0701 family protein |
| RA | 3,820,325 | T→C | 16.6% | R282R (CGA→CGG) | ligB ← | DNA ligase, NAD(+)‑dependent |
| RA | 3,838,902 | C→T | 11.4% | L219L (CTG→TTG) | yicL → | EamA family inner membrane putative transporter |
| RA | 3,875,521 | T→C | 17.9% | A28A (GCT→GCC) | yidX → | putative lipoprotein |
| RA | 3,879,936 | T→G | 22.3% | T62P (ACC→CCC) | gyrB ← | DNA gyrase, subunit B |
| RA | 3,983,147 | C→A | 9.5% | Q64K (CAA→AAA) | aslB → | putative AslA‑specific sulfatase‑maturating enzyme |
| RA | 3,983,165 | A→C | 13.6% | T70P (ACC→CCC) | aslB → | putative AslA‑specific sulfatase‑maturating enzyme |
| JC | 4,001,645 | Δ5 bp | 100% | coding (220‑224/951 nt) | corA → | magnesium/nickel/cobalt transporter |
| RA | 4,043,014 | A→G | 23.5% | G200G (GGA→GGG) | srkA → | Cpx stress response Thr/Ser protein kinase; MazF antagonist protein |
| RA | 4,098,366 | C→A | 15.4% | Q211K (CAA→AAA) | rhaS → | transcriptional activator of rhaBAD and rhaT |
| RA | 4,103,633 | A→C | 17.8% | V448G (GTG→GGG) | cpxA ← | sensory histidine kinase in two‑component regulatory system with CpxR |
| RA | 4,138,037 | A→C | 17.8% | G333G (GGT→GGG) | gldA ← | glycerol dehydrogenase, NAD+ dependent; 1,2‑propanediol:NAD+ oxidoreductase |
| RA | 4,143,145 | A→G | 13.9% | I206V (ATT→GTT) | frwC → | putative enzyme IIC component of PTS |
| RA | 4,160,854 | C→T | 20.9% | intergenic (‑64/‑270) | sthA ← / → fabR | pyridine nucleotide transhydrogenase, soluble/transcriptional repressor of fabA and fabB |
| RA | 4,184,543 | C→A | 100% | P1100Q (CCG→CAG) | rpoB → | RNA polymerase, beta subunit |
| RA | 4,296,060 | C→T | 22.2% | intergenic (+266/+376) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,268 | T→C | 21.0% | intergenic (+474/+168) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,380:1 | +CG | 100% | intergenic (+586/+56) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,300,840 | A→G | 10.2% | L64P (CTC→CCC) | mdtP ← | outer membrane factor of efflux pump |
| RA | 4,368,875 | A→G | 25.3% | E71G (GAG→GGG) | fxsA → | suppressor of F exclusion of phage T7 |
| RA | 4,428,194 | A→C | 9.4% | V175G (GTG→GGG) | ytfB ← | OapA family protein |
| RA | 4,440,923 | T→C | 8.3% | E98G (GAG→GGG) | ytfL ← | UPF0053 family inner membrane protein |
| RA | 4,537,714 | A→C | 15.1% | V351G (GTG→GGG) | nanM ← | N‑acetylneuraminic acid mutarotase |
| RA | 4,579,656 | A→C | 17.4% | V62G (GTG→GGG) | symE ← | toxic peptide regulated by antisense sRNA symR |
| RA | 4,594,557 | G→A | 20.3% | L56F (CTC→TTC) | lgoT ← | putative L‑galactonate:H+ symporter |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 997558 | 997840 | 283 | 25 [21] | [21] 22 | ssuE/elfA | NAD(P)H‑dependent FMN reductase/laminin‑binding fimbrin subunit |
| * | * | ÷ | NC_000913 | 1530053 | 1530400 | 348 | 22 [16] | [15] 22 | ydcD | putative immunity protein for RhsE |
| * | * | ÷ | NC_000913 | 2033790 | 2034018 | 229 | 23 [19] | [21] 22 | rseX/yedS | sRNA antisense regulator of ompA and ompC translation, Hfq‑dependent/pseudogene, outer membrane protein homology; putative outer membrane protein |
| * | * | ÷ | NC_000913 | 2469262 | 2469801 | 540 | 23 [21] | [21] 22 | gtrS | serotype‑specific glucosyl transferase, CPS‑53 (KpLE1) prophage |
| * | * | ÷ | NC_000913 | 2629599 | 2629797 | 199 | 22 [21] | [18] 24 | [yfgH] | [yfgH] |
| * | * | ÷ | NC_000913 | 3172146 | 3172228 | 83 | 23 [21] | [19] 22 | [ygiZ] | [ygiZ] |
| * | * | ÷ | NC_000913 | 3769624 | 3769948 | 325 | 22 [21] | [21] 23 | [yibV]–[yibU] | [yibV],yibV,[yibU] |
| * | * | ÷ | NC_000913 | 3798992 | 3799535 | 544 | 23 [21] | [21] 23 | [waaU]–[waaZ] | [waaU],[waaZ] |
| * | * | ÷ | NC_000913 | 4233737 | 4235444 | 1708 | 23 [21] | [21] 22 | pgi | pgi |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 1207790 = | 15 (0.180) | 79 (1.050) | 54/392 | NT | 87.8% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | 1209619 = | 8 (0.110) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | 1207795 = | 14 (0.170) | 3 (0.040) +C |
3/422 | NT | 20.1% | coding (295/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | 1209615 = | 10 (0.120) | pseudogene (5/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 14 (0.170) | 83 (1.110) | 55/392 | NT | 88.8% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | = 1209602 | 8 (0.110) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||