mutation predictions | marginal predictions | summary statistics | genome diff | command line log
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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 | 91,554 | A→G | I48V (ATC→GTC) | ftsI → | transpeptidase involved in septal peptidoglycan synthesis; penicillin‑binding protein 3 |
| RA | 91,816 | G→A | R135H (CGC→CAC) | ftsI → | transpeptidase involved in septal peptidoglycan synthesis; penicillin‑binding protein 3 |
| RA | 107,553 | (T)9→8 | intergenic (+79/‑152) | lpxC → / → secM | UDP‑3‑O‑acyl N‑acetylglucosamine deacetylase/regulator of secA translation |
| MC JC | 257,908 | Δ776 bp | [crl] | [crl] | |
| RA | 281,599 | C→T | G129S (GGC→AGC) | yagA ← | CP4‑6 prophage; putative DNA‑binding transcriptional regulator |
| 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 | 460,106 | A→T | I407F (ATC→TTC) | lon → | DNA‑binding ATP‑dependent protease La |
| RA | 632,971 | C→T | A169A (GCG→GCA) | ybdH ← | putative oxidoreductase |
| RA | 780,758 | T→C | intergenic (+129/‑7) | lysT → / → valT | tRNA‑Lys/tRNA‑Val |
| RA | 953,802 | A→G | V222A (GTA→GCA) | focA ← | formate channel |
| RA | 1,077,116 | T→C | E589E (GAA→GAG) | putA ← | fused DNA‑binding transcriptional regulator/proline dehydrogenase/pyrroline‑5‑carboxylate dehydrogenase |
| RA | 1,143,641 | G→A | H243Y (CAT→TAT) | rne ← | endoribonuclease; RNA‑binding protein;RNA degradosome binding protein |
| RA | 1,146,997 | G→A | T68T (ACG→ACA) | yceD → | DUF177 family protein |
| RA | 1,246,073 | C→T | G435D (GGC→GAC) | treA ← | periplasmic trehalase |
| RA | 1,312,192 | T→C | M19V (ATG→GTG) | yciA ← | acyl‑CoA esterase |
| RA | 1,489,197 | C→T | D322D (GAC→GAT) | aldA → | aldehyde dehydrogenase A, NAD‑linked |
| RA | 1,554,731 | C→T | M313I (ATG→ATA) | maeA ← | malate dehydrogenase, decarboxylating, NAD‑requiring; malic enzyme |
| RA | 1,597,313 | (C)7→8 | pseudogene (675/3861 nt) | yneO ← | pseudogene, AidA homolog |
| RA | 1,755,639 | G→A | intergenic (‑498/‑59) | ydhZ ← / → pykF | uncharacterized protein/pyruvate kinase I |
| RA | 1,853,467 | (A)7→8 | coding (513/1359 nt) | ydjE ← | putative MFS sugar transporter, membrane protein |
| RA | 1,868,250 | A→G | Y448C (TAC→TGC) | yeaG → | protein kinase, endogenous substrate unidentified; autokinase |
| RA | 1,946,025 | (A)7→6 | intergenic (‑49/+90) | ruvA ← / ← yobI | component of RuvABC resolvasome, regulatory subunit/uncharacterized 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 | 2,173,363 | 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 | 2,225,764 | T→C | intergenic (‑133/‑37) | yohC ← / → yohD | Yip1 family inner membrane protein/DedA family inner membrane protein |
| RA | 2,238,103 | T→C | K396R (AAA→AGA) | mglA ← | methyl‑galactoside ABC transporter ATPase |
| RA | 2,326,925 | (C)6→7 | coding (817/1185 nt) | atoB → | acetyl‑CoA acetyltransferase |
| 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 | 2,531,596 | (G)6→5 | coding (134/762 nt) | cysZ → | sulfate transporter, sulfite inhibited |
| RA | 2,554,244 | G→A | D313D (GAC→GAT) | eutR ← | eut operon transcriptional activator, AraC family |
| 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 | 2,765,014 | T→C | D47G (GAC→GGC) | yfjL ← | CP4‑57 putative defective prophage, DUF4297/DUF1837 polymorphic toxin family protein |
| RA | 2,809,774 | (T)7→8 | coding (158/738 nt) | ygaZ → | putative L‑valine exporter, norvaline resistance protein |
| RA | 2,838,784 | A→G | C161R (TGC→CGC) | ascG ← | asc operon transcriptional repressor; prpBC operon repressor |
| RA | 2,866,592 | +C | coding (960/993 nt) | rpoS ← | RNA polymerase, sigma S (sigma 38) factor |
| RA | 2,890,521 | G→A | P460S (CCA→TCA) | cysJ ← | sulfite reductase, alpha subunit, flavoprotein |
| RA | 2,976,311 | (A)8→7 | intergenic (‑297/‑288) | aas ← / → galR | fused 2‑acylglycerophospho‑ethanolamine acyl transferase/acyl‑acyl carrier protein synthetase/galactose‑inducible d‑galactose regulon transcriptional repressor; autorepressor |
| RA | 3,008,075 | A→G | D189G (GAC→GGC) | ygeX → | 2,3‑diaminopropionate ammonia lyase, PLP‑dependent |
| RA | 3,086,935 | G→T | G77V (GGC→GTC) | metK → | S‑adenosylmethionine synthetase |
| RA | 3,194,516 | A→G | K551K (AAA→AAG) | yqiK → | PHB family membrane protein, function unknown |
| RA | 3,277,706 | (A)7→6 | coding (370/465 nt) | yhaV → | toxin of the SohB(PrlF)‑YhaV toxin‑antitoxin system |
| 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 | 3,453,105 | G→A | H56Y (CAC→TAC) | rpsJ ← | 30S ribosomal subunit protein S10 |
| RA | 3,542,503 | G→A | W699* (TGG→TGA) | 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 |
| MC JC | 3,582,206 | Δ1,222 bp | IS1‑mediated | [yhhZ]–yrhA | [yhhZ], yrhA |
| JC | 3,596,220 | (TCA)3→2 | coding (182‑184/927 nt) | livH ← | branched‑chain amino acid ABC transporter permease |
| 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 | 3,966,720 | C→T | R102C (CGC→TGC) | rho → | transcription termination factor |
| RA | 4,121,597 | (T)5→4 | coding (151/1332 nt) | hslU ← | molecular chaperone and ATPase component of HslUV protease |
| RA | 4,185,211 | T→C | F1323L (TTC→CTC) | rpoB → | RNA polymerase, beta subunit |
| RA | 4,215,147 | A→C | N290H (AAC→CAC) | 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 | 4,370,616 | A→G | intergenic (‑204/‑72) | yjeH ← / → groS | putative transporter/Cpn10 chaperonin GroES, small subunit of GroESL |
| 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 | 4,411,047 | C→T | S165S (AGC→AGT) | yjfJ → | PspA/IM30 family protein |
| RA | 4,465,236 | C→T | P315P (CCG→CCA) | treB ← | trehalose‑specific PTS enzyme: IIB and IIC component |
| RA | 4,494,883 | (A)7→8 | coding (261/564 nt) | idnK → | D‑gluconate kinase, thermosensitive |
| RA | 4,548,150 | A→G | T137A (ACG→GCG) | fimF → | minor component of type 1 fimbriae |
| 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 | 780791 | 781085 | 295 | 58 [56] | [57] 58 | [valT]–[valZ] | [valT], lysW, [valZ] |
| * | * | ÷ | NC_000913 | 3423712–3424234 | 3424604–3424238 | 5–893 | 58 [57] | [57] 59 | [rrfD]–[rrlD] | [rrfD], [rrlD] |
| * | * | ÷ | NC_000913 | 3621158–3622298 | 3622645–3622421 | 124–1488 | 58 [55] | [57] 60 | rhsB | Rhs protein with DUF4329 family putative toxin domain; putative neighboring cell growth inhibitor |
| * | * | ÷ | NC_000913 | 3762301–3764074 | 3765222–3764077 | 4–2922 | 59 [55] | [54] 58 | rhsA | Rhs protein with putative toxin 55 domain; putative polysaccharide synthesis/export protein; putative neighboring cell growth inhibitor |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 151 (1.350) | 94/190 | 0.0 | 99.7% | intergenic (+253/‑1684) | ychE/oppA | UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein |
| ? | NC_000913 | 1300698 = | 1 (0.010) | intergenic (+1453/‑484) | ychE/oppA | UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein | |||||