mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.29.0 revision 8f9c342918e4
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Predicted mutations | |||||
|---|---|---|---|---|---|
| evidence | position | mutation | annotation | gene | description |
| RA | 55,620 | A→G | M497T (ATG→ACG) | lptD ← | LPS assembly OM complex LptDE, beta‑barrel component |
| RA | 107,553 | (T)9→8 | intergenic (+79/‑152) | lpxC → / → secM | UDP‑3‑O‑acyl N‑acetylglucosamine deacetylase/regulator of secA translation |
| RA | 160,864 | (C)6→7 | coding (623/705 nt) | sfsA ← | sugar fermentation stimulation protein A |
| RA | 220,255 | Δ1 bp | coding (674/816 nt) | metQ ← | DL‑methionine transporter subunit |
| RA | 236,569 | C→T | A168V (GCC→GTC) | dnaQ → | DNA polymerase III epsilon subunit |
| MC JC | 257,908 | Δ776 bp | [crl] | [crl] | |
| RA | 259,346 | C→A | R252L (CGC→CTC) | phoE ← | outer membrane phosphoporin protein E |
| RA | 270,287 | (A)7→8 | pseudogene (10/258 nt) | insN → | pseudogene, IS911 transposase A;IS, phage, Tn; Transposon‑related functions; extrachromosomal; transposon related |
| RA | 380,021 | (G)10→8 | intergenic (‑140/+47) | frmR ← / ← yaiO | regulator protein that represses frmRAB operon/outer membrane protein |
| RA | 410,479 | A→G | S112S (TCA→TCG) | mak → | manno(fructo)kinase |
| RA | 420,149 | Δ1 bp | coding (559/1320 nt) | brnQ → | branched‑chain amino acid transport system 2 carrier protein; LIV‑II transport system for Ile, Leu, and Val |
| RA | 426,471 | G→A | R112H (CGT→CAT) | tgt → | tRNA‑guanine transglycosylase |
| RA | 432,193 | +G | intergenic (‑180/+119) | tsx ← / ← yajI | nucleoside channel, receptor of phage T6 and colicin K/putative lipoprotein |
| RA | 434,614 | (C)6→7 | intergenic (+56/‑33) | ribD → / → ribE | fused diaminohydroxyphosphoribosylaminopyrimidine deaminase and 5‑amino‑6‑(5‑phosphoribosylamino) uracil reductase/riboflavin synthase beta chain |
| RA | 467,839 | T→C | V143A (GTC→GCC) | cof → | thiamine pyrimidine pyrophosphate hydrolase; HMP‑PP phosphatase |
| RA | 542,233 | (G)5→4 | coding (346/1146 nt) | glxK → | glycerate kinase II |
| RA | 560,553 | C→T | A286V (GCC→GTC) | sfmD → | putative outer membrane export usher protein |
| RA | 561,696 | (G)6→7 | coding (2000/2604 nt) | sfmD → | putative outer membrane export usher protein |
| RA | 705,972 | (T)9→10 | intergenic (+82/‑121) | nagE → / → glnS | N‑acetyl glucosamine specific PTS enzyme IIC, IIB, and IIA components/glutamyl‑tRNA synthetase |
| RA | 715,849 | A→G | L146L (TTA→TTG) | ybfP → | lipoprotein |
| RA | 755,958 | G→A | A18T (GCA→ACA) | sdhA → | succinate dehydrogenase, flavoprotein subunit |
| RA | 933,690 | C→T | P156L (CCA→CTA) | ftsK → | DNA translocase at septal ring sorting daughter chromsomes |
| RA | 953,802 | A→G | V222A (GTA→GCA) | focA ← | formate channel |
| RA | 1,004,160 | (G)7→8 | coding (214/711 nt) | ycbF → | putative periplasmic pilin chaperone |
| RA | 1,053,516 | (G)6→7 | coding (2663/2745 nt) | torS ← | hybrid sensory histidine kinase in two‑component regulatory system with TorR |
| RA | 1,079,293 | (T)6→5 | intergenic (‑411/‑12) | putA ← / → putP | fused DNA‑binding transcriptional regulator/proline dehydrogenase/pyrroline‑5‑carboxylate dehydrogenase/proline:sodium symporter |
| RA | 1,143,641 | G→A | H243Y (CAT→TAT) | rne ← | endoribonuclease; RNA‑binding protein;RNA degradosome binding protein |
| RA | 1,148,639 | A→G | Y340C (TAC→TGC) | plsX → | putative phosphate acyltransferase |
| RA | 1,168,850 | T→C | intergenic (‑18/‑223) | ycfQ ← / → bhsA | repressor for bhsA(ycfR)/biofilm, cell surface and signaling protein |
| RA | 1,197,853 | T→C | N129D (AAT→GAT) | ymfE ← | e14 prophage; putative inner membrane protein |
| RA | 1,212,088 | (C)8→7 | intergenic (‑85/+615) | iraM ← / ← ycgX | RpoS stabilzer during Mg starvation, anti‑RssB factor/DUF1398 family protein |
| RA | 1,218,196 | A→G | H290R (CAC→CGC) | ycgG → | putative membrane‑anchored cyclic‑di‑GMP phosphodiesterase |
| RA | 1,245,862 | (C)6→7 | coding (1515/1698 nt) | treA ← | periplasmic trehalase |
| RA | 1,246,073 | C→T | G435D (GGC→GAC) | treA ← | periplasmic trehalase |
| RA | 1,287,820 | G→A | R269C (CGC→TGC) | purU ← | formyltetrahydrofolate hydrolase |
| RA | 1,329,743 | G→A | V138M (GTG→ATG) | sohB → | inner membrane protein, S49 peptidase family protein |
| RA | 1,346,794 | A→G | intergenic (‑52/‑2) | gmr ← / → ymiB | cyclic‑di‑GMP phosphodiesterase; csgD regulator; modulator of RNase II stability/uncharacterized protein |
| RA | 1,489,197 | C→T | D322D (GAC→GAT) | aldA → | aldehyde dehydrogenase A, NAD‑linked |
| RA | 1,507,246 | A→G | T156A (ACG→GCG) | ydcP → | putative peptidase |
| RA | 1,543,754 | T→C | T103A (ACG→GCG) | narU ← | nitrate/nitrite transporter |
| RA | 1,594,256 | (C)8→7 | pseudogene (3732/3861 nt) | yneO ← | pseudogene, AidA homolog |
| JC | 1,597,236 | Δ7 bp | pseudogene (746‑752/3861 nt) | yneO ← | pseudogene, AidA homolog |
| RA | 1,610,183 | G→A | I166I (ATC→ATT) | uxaB ← | altronate oxidoreductase, NAD‑dependent |
| RA | 1,698,281 | A→G | V300V (GTT→GTC) | malI ← | transcriptional repressor of Mal regulon |
| RA | 1,755,639 | G→A | intergenic (‑498/‑59) | ydhZ ← / → pykF | uncharacterized protein/pyruvate kinase I |
| RA | 1,757,705 | (T)8→7 | intergenic (+48/+16) | lpp → / ← ldtE | murein lipoprotein/murein L,D‑transpeptidase |
| RA | 1,806,042 | (C)6→5 | coding (42/759 nt) | ydiY ← | acid‑inducible putative outer membrane protein |
| RA | 1,807,923 | (T)6→5 | coding (128/861 nt) | yniA → | fructosamine kinase family protein |
| RA | 1,868,250 | A→G | Y448C (TAC→TGC) | yeaG → | protein kinase, endogenous substrate unidentified; autokinase |
| RA | 1,903,571 | A→G | T164A (ACC→GCC) | manY → | mannose‑specific enzyme IIC component of PTS |
| RA | 1,925,932 | (T)7→6 | coding (493/657 nt) | yobB → | C‑N hydrolase family protein |
| MC JC | 1,978,503 | Δ776 bp | insB1–insA | insB1, insA | |
| JC JC | 1,979,486 | IS5 (+) +4 bp | intergenic (‑271/‑264) | insA ← / → uspC | IS1 repressor TnpA/universal stress protein |
| RA | 2,018,260 | (A)8→7 | coding (315/444 nt) | fliJ → | flagellar protein |
| RA | 2,065,747 | (C)6→5 | coding (18/546 nt) | cobU ← | cobinamide kinase and cobinamide phosphate guanylyltransferase |
| RA | 2,075,357 | (A)6→5 | coding (579/1533 nt) | yeeR → | CP4‑44 prophage; putative membrane protein |
| 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 | 2,185,875 | (G)7→8 | intergenic (‑79/‑42) | rcnR ← / → rcnA | transcriptional repressor of rcnA/membrane protein conferring nickel and cobalt resistance |
| 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 | 2,300,930 | T→C | E608E (GAA→GAG) | napA ← | nitrate reductase, periplasmic, large subunit |
| RA | 2,399,911 | T→C | K85K (AAA→AAG) | nuoG ← | NADH:ubiquinone oxidoreductase, chain G |
| RA | 2,412,632 | (A)8→7 | intergenic (‑38/+45) | yfbU ← / ← yfbV | UPF0304 family protein/UPF0208 family inner membrane protein |
| RA | 2,413,482 | T→C | L5L (TTA→CTA) | ackA → | acetate kinase A and propionate kinase 2 |
| RA | 2,440,991 | A→G | G205G (GGT→GGC) | fabB ← | 3‑oxoacyl‑[acyl‑carrier‑protein] synthase I |
| RA | 2,469,733 | (T)8→7 | coding (603/1332 nt) | gtrS → | serotype‑specific glucosyl transferase, CPS‑53 (KpLE1) prophage |
| RA | 2,470,410 | (T)7→6 | coding (1280/1332 nt) | gtrS → | serotype‑specific glucosyl transferase, CPS‑53 (KpLE1) prophage |
| RA | 2,516,689 | T→C | T382A (ACG→GCG) | yfeA ← | putative diguanylate cyclase |
| RA | 2,533,408 | (A)6→5 | intergenic (+28/‑356) | cysK → / → ptsH | cysteine synthase A, O‑acetylserine sulfhydrolase A subunit/phosphohistidinoprotein‑hexose phosphotransferase component of PTS system (Hpr) |
| RA | 2,553,210 | A→G | K287E (AAA→GAA) | amiA → | N‑acetylmuramoyl‑l‑alanine amidase I |
| RA | 2,589,100 | (A)6→5 | coding (1506/3114 nt) | acrD → | aminoglycoside/multidrug efflux system |
| RA | 2,611,005 | (C)5→6 | coding (300/759 nt) | hyfI → | hydrogenase 4, Fe‑S subunit |
| RA | 2,652,855 | (G)6→7 | coding (362/846 nt) | sseA → | 3‑mercaptopyruvate sulfurtransferase |
| RA | 2,731,312 | G→A | intergenic (‑155/+288) | rrsG ← / ← clpB | 16S ribosomal RNA of rrnG operon/protein disaggregation chaperone |
| RA | 2,734,543 | (C)8→7 | coding (492/732 nt) | yfiH ← | UPF0124 family protein |
| RA | 2,754,784 | (A)8→9 | intergenic (‑20/‑112) | ratA ← / → smpB | toxic UPF0083 family protein inhibitor of 70S ribosome formation/tmRNA‑binding trans‑translation protein |
| RA | 2,760,118 | G→A | W378* (TGG→TGA) | yfjI → | CP4‑57 prophage; uncharacterized protein |
| JC | 2,765,463 | (TATGGCAC)6→8 | intergenic (‑310/+50) | yfjL ← / ← yfjM | CP4‑57 putative defective prophage, DUF4297/DUF1837 polymorphic toxin family protein/CP4‑57 prophage; uncharacterized protein |
| RA | 2,809,774 | (T)7→8 | coding (158/738 nt) | ygaZ → | putative L‑valine exporter, norvaline resistance protein |
| RA | 2,866,592 | +C | coding (960/993 nt) | rpoS ← | RNA polymerase, sigma S (sigma 38) factor |
| RA | 2,923,182 | T→C | L201L (CTA→CTG) | truC ← | tRNA(Ile1,Asp) pseudouridine(65) synthase |
| RA | 2,950,330 | G→A | M363I (ATG→ATA) | argA → | amino acid N‑acetyltransferase and inactive acetylglutamate kinase |
| RA | 2,966,413 | A→T | D674E (GAT→GAA) | ptsP ← | PEP‑protein phosphotransferase enzyme I; GAF domain containing protein |
| RA | 2,972,860 | (T)7→6 | coding (1003/1194 nt) | lplT ← | lysophospholipid transporter |
| RA | 3,008,075 | A→G | D189G (GAC→GGC) | ygeX → | 2,3‑diaminopropionate ammonia lyase, PLP‑dependent |
| RA | 3,070,123 | (A)7→6 | intergenic (‑316/+42) | mscS ← / ← fbaA | mechanosensitive channel protein, small conductance/fructose‑bisphosphate aldolase, class II |
| RA | 3,101,039 | (C)7→6 | coding (585/720 nt) | yggN ← | DUF2884 family putative periplasmic protein |
| RA | 3,182,712 | G→A | A55T (GCC→ACC) | zupT → | zinc transporter |
| RA | 3,194,516 | A→G | K551K (AAA→AAG) | yqiK → | PHB family membrane protein, function unknown |
| RA | 3,352,673 | T→C | E118G (GAA→GGA) | arcB ← | aerobic respiration control sensor histidine protein kinase, cognate to two‑component response regulators ArcA and RssB |
| RA | 3,379,266 | (C)7→8 | coding (732/1128 nt) | zapE ← | divisome ATPase |
| RA | 3,411,299 | T→C | V10A (GTA→GCA) | fis → | global DNA‑binding transcriptional dual regulator |
| RA | 3,467,120 | A→G | intergenic (‑129/+40) | bfd ← / ← chiA | bacterioferritin‑associated ferredoxin/periplasmic endochitinase |
| RA | 3,499,708 | (C)5→4 | intergenic (+93/‑202) | yhfL → / → frlA | small lipoprotein/putative fructoselysine transporter |
| RA | 3,512,561 | Δ1 bp | intergenic (‑217/+73) | yhfZ ← / ← trpS | putative DNA‑binding transcriptional regulator/tryptophanyl‑tRNA synthetase |
| RA | 3,541,493 | T→C | F363L (TTC→CTC) | feoB → | ferrous iron transporter protein B and GTP‑binding protein; membrane protein |
| RA | 3,542,093 | G→A | V563M (GTG→ATG) | feoB → | ferrous iron transporter protein B and GTP‑binding protein; membrane 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 | 3,580,930 | (A)9→8 | intergenic (‑125/‑208) | yhhX ← / → yhhY | putative oxidoreductase/aminoacyl nucleotide detoxifying acetyltransferase |
| MC JC | 3,582,206 | Δ1,222 bp | IS1‑mediated | [yhhZ]–yrhA | [yhhZ], yrhA |
| RA | 3,595,315 | (A)5→4 | coding (166/1278 nt) | livM ← | branched‑chain amino acid ABC transporter permease |
| RA | 3,645,196 | G→A | intergenic (‑14/‑189) | prlC ← / → rlmJ | oligopeptidase A/23S rRNA m(6)A2030 methyltransferase, SAM‑dependent |
| RA | 3,648,144 | (T)7→6 | intergenic (‑356/‑384) | dinQ ← / → arsR | UV‑inducible membrane toxin, DinQ‑AgrB type I toxin‑antitoxin system/arsenical resistance operon transcriptional repressor; autorepressor |
| RA | 3,671,943 | G→C | intergenic (‑49/‑471) | yhjB ← / → yhjC | putative DNA‑binding transcriptional response regulator/LysR family putative transcriptional regulator |
| RA | 3,714,073 | C→T | P141L (CCG→CTG) | yiaC → | GNAT family putative N‑acetyltransferase |
| RA | 3,742,218 | A→G | A105A (GCT→GCC) | yiaJ ← | transcriptional repressor for the yiaKLMNO‑lyxK‑sgbHUE operon |
| RA | 3,811,584 | G→A | P31S (CCG→TCG) | rpmB ← | 50S ribosomal subunit protein L28 |
| MC JC | 3,815,859 | Δ82 bp | [rph]–[rph] | [rph], [rph] | |
| RA | 3,952,380 | G→A | L60L (CTG→CTA) | ilvM → | acetolactate synthase 2 small subunit |
| RA | 3,952,569 | C→T | A29V (GCG→GTG) | ilvE → | branched‑chain amino acid aminotransferase |
| RA | 4,002,325 | C→T | I300I (ATC→ATT) | corA → | magnesium/nickel/cobalt transporter |
| RA | 4,100,447 | (T)6→5 | coding (79/1035 nt) | rhaT ← | L‑rhamnose:proton symporter |
| RA | 4,105,411 | A→G | V87A (GTT→GCT) | cpxR ← | response regulator in two‑component regulatory system with CpxA |
| RA | 4,128,259 | A→G | V46A (GTG→GCG) | metJ ← | transcriptional repressor, S‑adenosylmethionine‑binding |
| RA | 4,200,184 | (A)7→5 | intergenic (+90/‑96) | yjaG → / → hupA | DUF416 domain protein/HU, DNA‑binding transcriptional regulator, alpha subunit |
| RA | 4,214,964 | A→G | I229V (ATT→GTT) | metA → | homoserine O‑transsuccinylase |
| RA | 4,227,628 | (A)5→4 | intergenic (+117/‑103) | metH → / → yjbB | homocysteine‑N5‑methyltetrahydrofolate transmethylase, B12‑dependent/putative Na+/Pi‑cotransporter |
| RA | 4,296,060 | C→T | intergenic (+266/+376) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,381 | +GC | intergenic (+587/+55) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,337,024 | G→A | S3L (TCG→TTG) | adiC ← | arginine:agmatine antiporter |
| RA | 4,343,821 | (T)7→6 | coding (453/1422 nt) | melB → | melibiose:sodium symporter |
| RA | 4,370,616 | A→G | intergenic (‑204/‑72) | yjeH ← / → groS | putative transporter/Cpn10 chaperonin GroES, small subunit of GroESL |
| RA | 4,382,091 | C→T | W76* (TGG→TGA) | frdA ← | anaerobic fumarate reductase catalytic and NAD/flavoprotein subunit |
| RA | 4,397,557 | G→T | G49V (GGT→GTT) | mutL → | methyl‑directed mismatch repair protein |
| RA | 4,408,903 | (A)6→5 | coding (2250/2442 nt) | rnr → | exoribonuclease R, RNase R |
| 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 | 4,467,129 | C→T | E40K (GAA→AAA) | treR ← | trehalose 6‑phosphate‑inducible trehalose regulon transcriptional repressor |
| RA | 4,494,883 | (A)7→8 | coding (261/564 nt) | idnK → | D‑gluconate kinase, thermosensitive |
| RA | 4,503,169 | (G)5→4 | coding (263/1329 nt) | insG ← | IS4 transposase |
| RA | 4,517,951 | (C)6→7 | coding (285/522 nt) | fecI ← | RNA polymerase sigma‑19 factor, fec operon‑specific; ECF sigma factor |
| RA | 4,573,528 | A→G | pseudogene (1115/1503 nt) | yjiT → | pseudogene |
| RA | 4,606,215 | (G)8→7 | noncoding (72/87 nt) | leuP ← | tRNA‑Leu |
| RA | 4,638,193 | (C)6→7 | coding (16/1353 nt) | creD → | inner membrane protein |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 3621155–3622298 | 3622641–3622421 | 124–1487 | 65 [62] | [62] 64 | rhsB | Rhs protein with DUF4329 family putative toxin domain; putative neighboring cell growth inhibitor |
| * | * | ÷ | NC_000913 | 3943434–3943987 | 3945525–3943992 | 6–2092 | 65 [61] | [62] 63 | gltU–[rrlC] | gltU, [rrlC] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 171 (1.540) | 102/190 | 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 | |||||
| * | ? | NC_000913 | = 4171911 | NA (NA) | 108 (1.170) | 70/158 | 0.1 | 99.3% | intergenic (+155/‑146) | rrfB/murB | 5S ribosomal RNA of rrnB operon/UDP‑N‑acetylenolpyruvoylglucosamine reductase, FAD‑binding |
| ? | NC_000913 | 4213147 = | 1 (0.010) | noncoding (108/120 nt) | rrfE | 5S ribosomal RNA of rrnE operon | |||||