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 | 60,316 | C→T | E11K (GAA→AAA) | rluA ← | dual specificity 23S rRNA pseudouridine(746), tRNA pseudouridine(32) synthase, SAM‑dependent |
| RA | 61,175 | (T)5→4 | coding (2090/2907 nt) | rapA ← | RNA polymerase remodeling/recycling factor ATPase; RNA polymerase‑associated, ATP‑dependent RNA translocase |
| RA | 107,553 | (T)9→8 | intergenic (+79/‑152) | lpxC → / → secM | UDP‑3‑O‑acyl N‑acetylglucosamine deacetylase/regulator of secA translation |
| RA | 236,569 | C→T | A168V (GCC→GTC) | dnaQ → | DNA polymerase III epsilon subunit |
| MC JC | 257,908 | Δ776 bp | [crl] | [crl] | |
| RA | 282,417 | T→C | L47P (CTG→CCG) | yagE → | 2‑keto‑3‑deoxy gluconate (KDG) aldolase; CP4‑6 prophage |
| RA | 349,692 | A→G | intergenic (+120/‑320) | prpB → / → prpC | 2‑methylisocitrate lyase/2‑methylcitrate synthase |
| RA | 349,708 | C→T | intergenic (+136/‑304) | prpB → / → prpC | 2‑methylisocitrate lyase/2‑methylcitrate synthase |
| RA | 349,717 | T→C | intergenic (+145/‑295) | prpB → / → prpC | 2‑methylisocitrate lyase/2‑methylcitrate synthase |
| JC | 380,020 | (G)10→7 | intergenic (‑139/+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 | 420,471 | C→T | T294M (ACG→ATG) | 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 | 436,026 | G→A | T131T (ACG→ACA) | thiL → | thiamine monophosphate kinase |
| RA | 476,808 | T→C | V46A (GTA→GCA) | ybaA → | DUF1428 family protein |
| MC JC | 516,641 | (TGG)4→3 | coding (59‑61/780 nt) | fetB → | iron export ABC transporter permease; peroxide resistance protein |
| RA | 523,741 | (G)6→5 | coding (481/4281 nt) | rhsD → | Rhs protein with DUF4329 family putative toxin domain; putative neighboring cell growth inhibitor |
| RA | 561,696 | (G)6→7 | coding (2000/2604 nt) | sfmD → | putative outer membrane export usher protein |
| RA | 715,849 | A→G | L146L (TTA→TTG) | ybfP → | lipoprotein |
| RA | 953,802 | A→G | V222A (GTA→GCA) | focA ← | formate channel |
| RA | 957,203 | G→A | V148I (GTA→ATA) | ycaP → | UPF0702 family putative inner membrane protein |
| RA | 1,029,739 | (A)8→7 | coding (231/1191 nt) | rlmI ← | 23S rRNA m(5)C1962 methyltransferase, SAM‑dependent |
| RA | 1,053,516 | (G)6→7 | coding (2663/2745 nt) | torS ← | hybrid sensory histidine kinase in two‑component regulatory system with TorR |
| RA | 1,110,872 | A→G | T4A (ACA→GCA) | opgH → | OPG biosynthetic ACP‑dependent transmembrane UDP‑glucose beta‑1,2 glycosyltransferase; nutrient‑dependent cell size regulator, FtsZ assembly antagonist |
| RA | 1,143,641 | G→A | H243Y (CAT→TAT) | rne ← | endoribonuclease; RNA‑binding protein;RNA degradosome binding protein |
| RA | 1,163,714 | T→C | L152P (CTG→CCG) | thiK → | thiamine kinase |
| RA | 1,184,649 | A→G | Y316H (TAC→CAC) | potA ← | spermidine/putrescine ABC transporter ATPase |
| RA | 1,197,853 | T→C | N129D (AAT→GAT) | ymfE ← | e14 prophage; putative inner membrane protein |
| RA | 1,246,073 | C→T | G435D (GGC→GAC) | treA ← | periplasmic trehalase |
| RA | 1,370,044 | (T)9→8 | intergenic (+41/‑172) | pspE → / → ycjM | thiosulfate:cyanide sulfurtransferase (rhodanese)/alpha amylase catalytic domain family protein |
| RA | 1,407,343 | T→A | G151G (GGA→GGT) | ydaM ← | diguanylate cyclase, csgD regulator |
| RA | 1,420,793 | (G)6→7 | coding (110/423 nt) | ydaT → | Rac prophage; uncharacterized protein |
| RA | 1,489,197 | C→T | D322D (GAC→GAT) | aldA → | aldehyde dehydrogenase A, NAD‑linked |
| RA | 1,556,190 | C→T | V31I (GTC→ATC) | bdm ← | biofilm‑dependent modulation protein |
| RA | 1,580,714 | G→A | S26L (TCG→TTG) | ydeM ← | putative YdeN‑specific sulfatase‑maturating enzyme |
| RA | 1,594,132 | (C)8→9 | pseudogene (3856/3861 nt) | yneO ← | pseudogene, AidA homolog |
| RA | 1,594,256 | (C)8→7 | pseudogene (3732/3861 nt) | yneO ← | pseudogene, AidA homolog |
| RA | 1,698,281 | A→G | V300V (GTT→GTC) | malI ← | transcriptional repressor of Mal regulon |
| RA | 1,704,171 | G→A | D46D (GAC→GAT) | ydgJ ← | putative oxidoreductase |
| RA | 1,755,639 | G→A | intergenic (‑498/‑59) | ydhZ ← / → pykF | uncharacterized protein/pyruvate kinase I |
| RA | 1,847,724 | (C)6→7 | coding (285/1044 nt) | selD ← | selenophosphate synthase |
| 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 | 1,917,857 | G→A | S116S (TCG→TCA) | yebT → | MCE domain protein |
| RA | 1,942,523 | T→C | T21A (ACA→GCA) | znuA ← | zinc ABC transporter periplasmic binding protein |
| RA | 1,950,367 | A→T | D52E (GAT→GAA) | aspS ← | aspartyl‑tRNA synthetase |
| 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 | 1,984,734 | G→A | G112G (GGC→GGT) | araG ← | L‑arabinose ABC transporter ATPase |
| RA | 2,018,260 | (A)8→7 | coding (315/444 nt) | fliJ → | flagellar protein |
| RA | 2,143,684 | (G)6→7 | coding (419/3318 nt) | yegE → | putative diguanylate cyclase |
| 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 | 2,329,835 | G→A | pseudogene (4568/4605 nt) | yfaS ← | pseudogene, bacterial alpha2‑macroglobulin YfaS variant family; putative membrane protein |
| RA | 2,353,249 | T→C | H201H (CAT→CAC) | glpA → | anaerobic sn‑glycerol‑3‑phosphate dehydrogenase, large FAD/NAD(P)‑binding subunit |
| RA | 2,362,984 | A→G | I217T (ATC→ACC) | yfaY ← | inactive PncC family protein |
| 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 | 2,553,210 | A→G | K287E (AAA→GAA) | amiA → | N‑acetylmuramoyl‑l‑alanine amidase I |
| RA | 2,643,753 | G→A | G177G (GGC→GGT) | rlmN ← | dual specificity 23S rRNA m(2)A2503, tRNA m(2)A37 methyltransferase, SAM‑dependent |
| RA | 2,652,855 | (G)6→7 | coding (362/846 nt) | sseA → | 3‑mercaptopyruvate sulfurtransferase |
| RA | 2,676,572 | G→A | P85L (CCG→CTG) | yphD ← | putative sugar ABC transporter permease |
| RA | 2,679,503 | G→A | F1081F (TTC→TTT) | yphG ← | DUF4380 domain‑containing TPR repeat protein |
| RA | 2,731,312 | G→A | intergenic (‑155/+288) | rrsG ← / ← clpB | 16S ribosomal RNA of rrnG operon/protein disaggregation chaperone |
| RA | 2,809,774 | (T)7→8 | coding (158/738 nt) | ygaZ → | putative L‑valine exporter, norvaline resistance protein |
| RA | 2,854,144 | +G | coding (891/1011 nt) | hypE → | carbamoyl dehydratase, hydrogenases 1,2,3 maturation protein |
| RA | 2,866,592 | +C | coding (960/993 nt) | rpoS ← | RNA polymerase, sigma S (sigma 38) factor |
| RA | 2,917,114 | G→A | L686L (TTG→TTA) | barA → | hybrid sensory histidine kinase, in two‑component regulatory system with UvrY |
| RA | 2,967,707 | T→A | D243V (GAT→GTT) | ptsP ← | PEP‑protein phosphotransferase enzyme I; GAF domain containing protein |
| RA | 3,008,075 | A→G | D189G (GAC→GGC) | ygeX → | 2,3‑diaminopropionate ammonia lyase, PLP‑dependent |
| RA | 3,154,207 | (A)9→8 | coding (645/660 nt) | yghB → | general envelope maintenance protein; DedA family inner membrane protein; putative multidrug efflux transporter |
| 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 | 3,396,689 | G→A | S369S (AGC→AGT) | rng ← | ribonuclease G |
| RA | 3,411,299 | T→C | V10A (GTA→GCA) | fis → | global DNA‑binding transcriptional dual regulator |
| RA | 3,512,561 | Δ1 bp | intergenic (‑217/+73) | yhfZ ← / ← trpS | putative DNA‑binding transcriptional regulator/tryptophanyl‑tRNA synthetase |
| 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 | 3,597,846 | (T)5→4 | intergenic (‑286/‑138) | livK ← / → panM | leucine transporter subunit/PanD autocleavage accelerator, panothenate synthesis |
| 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 |
| MC JC | 3,815,859 | Δ82 bp | [rph]–[rph] | [rph], [rph] | |
| RA | 3,834,428 | (G)6→5 | coding (110/2319 nt) | yicI ← | putative alpha‑glucosidase |
| 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 | 4,103,886 | A→G | Y364H (TAT→CAT) | cpxA ← | sensory histidine kinase in two‑component regulatory system with CpxR |
| RA | 4,214,964 | A→G | I229V (ATT→GTT) | metA → | homoserine O‑transsuccinylase |
| 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 | 4,397,557 | G→T | G49V (GGT→GTT) | mutL → | methyl‑directed mismatch repair protein |
| 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 | 4,494,883 | (A)7→8 | coding (261/564 nt) | idnK → | D‑gluconate kinase, thermosensitive |
| RA | 4,573,528 | A→G | pseudogene (1115/1503 nt) | yjiT → | pseudogene |
| 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 | 3423710–3424234 | 3424595–3424239 | 6–886 | 37 [34] | [36] 38 | [rrfD]–[rrlD] | [rrfD], [rrlD] |
| * | * | ÷ | NC_000913 | 3621165–3622297 | 3622631–3622371 | 75–1467 | 38 [34] | [35] 37 | rhsB | Rhs protein with DUF4329 family putative toxin domain; putative neighboring cell growth inhibitor |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 1207790 = | 8 (0.110) | 58 (0.930) | 51/166 | 0.2 | 85.5% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | 1209619 = | 13 (0.210) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 9 (0.120) | 48 (0.770) | 41/166 | 0.7 | 82.4% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | = 1209602 | 13 (0.210) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 83 (1.160) | 58/190 | 0.2 | 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 | |||||