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 | 36,231 | T→C | intergenic (‑69/+40) | caiD ← / ← caiC | carnitinyl‑CoA dehydratase/putative crotonobetaine/carnitine‑CoA ligase |
| RA | 162,973 | G→A | C290Y (TGT→TAT) | hrpB → | putative ATP‑dependent helicase |
| JC | 190,553 | Δ14 bp | coding (680‑693/726 nt) | rpsB → | 30S ribosomal subunit protein S2 |
| RA | 216,568 | C→T | A146T (GCC→ACC) | yaeF ← | putative lipoprotein |
| RA | 236,541 | C→T | R159* (CGA→TGA) | dnaQ → | DNA polymerase III epsilon subunit |
| MC JC | 257,908 | Δ776 bp | [crl] | [crl] | |
| RA | 265,810 | T→A | Q93L (CAG→CTG) | ykfB ← | CP4‑6 prophage; uncharacterized protein |
| RA | 428,188 | G→T | R181L (CGC→CTC) | secD → | SecYEG protein translocase auxillary subunit |
| RA | 497,139 | (T)5→6 | intergenic (+145/‑36) | htpG → / → adk | protein refolding molecular co‑chaperone Hsp90, Hsp70‑dependent; heat‑shock protein; ATPase/adenylate kinase |
| RA | 520,993 | T→G | V193G (GTC→GGC) | ybbP → | putative ABC transporter permease |
| RA | 606,299 | A→T | V362E (GTG→GAG) | ybdK ← | weak gamma‑glutamyl:cysteine ligase |
| RA | 700,805 | A→T | C264S (TGC→AGC) | nagC ← | N‑acetylglucosamine‑inducible nag divergent operon transcriptional repressor |
| RA | 720,946 | C→T | intergenic (+106/+110) | ybfK → / ← kdpE | uncharacterized protein/response regulator in two‑component regulatory system with KdpD |
| RA | 756,886 | T→A | L327Q (CTG→CAG) | sdhA → | succinate dehydrogenase, flavoprotein subunit |
| RA | 772,209 | C→A | T251N (ACC→AAC) | cydA → | cytochrome d terminal oxidase, subunit I |
| RA | 882,722 | G→A | R5C (CGC→TGC) | deoR ← | deoxyribose‑5‑phosphate‑inducible deoxyribose operon transcriptional repressor; repressor of nupG and tsx |
| RA | 882,856 | C→A | R178L (CGT→CTT) | ybjG ← | undecaprenyl pyrophosphate phosphatase |
| RA | 894,155 | T→G | D124E (GAT→GAG) | potF → | putrescine ABC transporter periplasmic binding protein |
| RA | 1,075,612 | C→T | E1091K (GAA→AAA) | putA ← | fused DNA‑binding transcriptional regulator/proline dehydrogenase/pyrroline‑5‑carboxylate dehydrogenase |
| RA | 1,079,672 | G→A | R123H (CGC→CAC) | putP → | proline:sodium symporter |
| RA | 1,100,233 | G→A | intergenic (+39/‑63) | ycdY → / → ycdZ | redox enzyme maturation protein (REMP) chaperone for YcdX/DUF1097 family inner membrane protein |
| RA | 1,143,125 | C→T | D415N (GAC→AAC) | rne ← | endoribonuclease; RNA‑binding protein;RNA degradosome binding protein |
| RA | 1,193,289 | T→A | Q162L (CAG→CTG) | mnmA ← | tRNA(Gln,Lys,Glu) U34 2‑thiouridylase |
| RA | 1,197,739 | A→G | S167P (TCC→CCC) | ymfE ← | e14 prophage; putative inner membrane protein |
| RA | 1,292,944 | T→C | intergenic (‑22/‑583) | hns ← / → tdk | global DNA‑binding transcriptional dual regulator H‑NS/thymidine kinase/deoxyuridine kinase |
| RA | 1,315,705 | T→C | K22K (AAA→AAG) | yciF ← | putative rubrerythrin/ferritin‑like metal‑binding protein |
| RA | 1,401,844 | A→G | I471T (ATC→ACC) | abgB ← | p‑aminobenzoyl‑glutamate hydrolase, B subunit |
| RA | 1,413,709 | T→C | E11G (GAA→GGA) | ydaC ← | DUF1187 family protein, Rac prophage; putative double‑strand break reduction protein |
| RA | 1,434,459 | C→T | intergenic (‑235/+499) | ynaE ← / ← ttcC | cold shock protein, Rac prophage/pseudogene, prophage Rac integration site ttcA duplication;Phage or Prophage Related |
| RA | 1,460,438 | T→C | L462S (TTG→TCG) | paaH → | 3‑hydroxyadipyl‑CoA dehydrogenase, NAD+‑dependent |
| RA | 1,501,912 | T→A | I117I (ATT→ATA) | tehB → | tellurite, selenium methyltransferase, SAM‑dependent; tellurite, selenium resistance protein |
| RA | 1,519,159 | A→T | T45S (ACA→TCA) | curA → | curcumin/dihydrocurcumin reductase, NADPH‑dependent |
| RA | 1,529,300 | C→T | pseudogene (1399/2037 nt) | rhsE → | pseudogene, Rhs family |
| RA | 1,530,076 | (A)7→8 | coding (155/483 nt) | ydcD → | putative immunity protein for RhsE |
| RA | 1,580,094 | C→T | D233N (GAT→AAT) | ydeM ← | putative YdeN‑specific sulfatase‑maturating enzyme |
| RA | 1,580,128 | A→G | F221F (TTT→TTC) | ydeM ← | putative YdeN‑specific sulfatase‑maturating enzyme |
| RA | 1,665,195 | (T)7→8 | intergenic (+75/‑120) | dmsD → / → clcB | twin‑argninine leader‑binding protein for DmsA and TorA/H(+)/Cl(‑) exchange transporter |
| RA | 1,681,932 | T→C | P33P (CCA→CCG) | ydgC ← | GlpM family inner membrane protein |
| RA | 1,712,306 | (T)7→8 | intergenic (+148/‑463) | nth → / → dtpA | DNA glycosylase and apyrimidinic (AP) lyase (endonuclease III)/dipeptide and tripeptide permease A |
| RA | 1,712,518 | (C)6→5 | intergenic (+360/‑251) | nth → / → dtpA | DNA glycosylase and apyrimidinic (AP) lyase (endonuclease III)/dipeptide and tripeptide permease A |
| RA | 1,715,953 | T→C | K424E (AAA→GAA) | tyrS ← | tyrosyl‑tRNA synthetase |
| RA | 1,720,828 | C→T | intergenic (‑4/‑197) | slyA ← / → ydhI | global transcriptional regulator/DUF1656 family putative inner membrane efflux pump associated protein |
| RA | 1,728,444 | C→A | T33N (ACC→AAC) | rnt → | RNase T; exoribonuclease T; structured DNA 3' exonuclease; RNA processing; DNA repair |
| RA | 1,808,281 | (A)5→4 | coding (486/861 nt) | yniA → | fructosamine kinase family protein |
| RA | 1,827,031 | T→A | D410V (GAT→GTT) | astB ← | succinylarginine dihydrolase |
| RA | 1,946,955 | G→A | A141V (GCC→GTC) | ruvC ← | component of RuvABC resolvasome, endonuclease |
| RA | 1,983,761 | C→T | E437K (GAA→AAA) | araG ← | L‑arabinose ABC transporter ATPase |
| RA | 2,033,458 | T→G | I9I (ATA→ATC) | yedR ← | inner membrane protein |
| RA | 2,071,321 | A→G | intergenic (+110/‑218) | yeeP → / → flu | pseudogene, CP4‑44 prophage; 50S ribosome‑binding GTPase family;Phage or Prophage Related; putative histone/CP4‑44 prophage; antigen 43 (Ag43) phase‑variable biofilm formation autotransporter |
| 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 | 2,191,432 | C→T | G72S (GGC→AGC) | yehC ← | putative periplasmic pilin chaperone |
| RA | 2,210,811 | C→T | pseudogene (1712/2001 nt) | yehQ → | pseudogene |
| RA | 2,278,298 | C→T | intergenic (‑61/+272) | yejG ← / ← bcr | uncharacterized protein/bicyclomycin/cysteine/sulfonamide efflux transporter |
| RA | 2,281,279 | A→T | A216A (GCA→GCT) | yejH → | putative ATP‑dependent DNA or RNA helicase |
| RA | 2,436,937 | A→T | D305E (GAT→GAA) | pdxB ← | erythronate‑4‑phosphate dehydrogenase |
| RA | 2,469,656 | (T)7→8 | coding (526/1332 nt) | gtrS → | serotype‑specific glucosyl transferase, CPS‑53 (KpLE1) prophage |
| RA | 2,485,264 | G→A | W297* (TGG→TGA) | evgS → | hybrid sensory histidine kinase in two‑component regulatory system with EvgA |
| RA | 2,521,967 | C→A | A171S (GCG→TCG) | xapR ← | transcriptional activator of xapAB |
| RA | 2,563,518 | (A)5→6 | intergenic (+401/‑74) | yffP → / → yffQ | CPZ‑55 prophage; uncharacterized protein/CPZ‑55 prophage; uncharacterized protein |
| RA | 2,564,525 | G→A | M1M (ATG→ATA) † | yffS → | CPZ‑55 prophage; uncharacterized protein |
| RA | 2,600,288 | C→T | S128L (TCG→TTG) | gcvR → | transcriptional repressor, regulatory protein accessory to GcvA |
| RA | 2,810,756 | G→A | intergenic (+77/‑14) | ygaH → / → mprA | putative L‑valine exporter, norvaline resistance protein/transcriptional repressor of microcin B17 synthesis and multidrug efflux |
| RA | 2,810,758 | G→A | intergenic (+79/‑12) | ygaH → / → mprA | putative L‑valine exporter, norvaline resistance protein/transcriptional repressor of microcin B17 synthesis and multidrug efflux |
| RA | 2,817,931 | T→C | intergenic (‑71/+128) | argQ ← / ← argZ | tRNA‑Arg/tRNA‑Arg |
| RA | 2,852,356 | T→A | L74Q (CTG→CAG) | hypD → | hydrogenase maturation protein |
| RA | 2,887,352 | T→A | intergenic (‑133/+226) | ygcB ← / ← cysH | Cascade complex anti‑viral R‑loop helicase‑annealase Cas3/phosphoadenosine phosphosulfate reductase; PAPS reductase, thioredoxin dependent |
| RA | 3,410,649 | A→G | I124V (ATC→GTC) | dusB → | tRNA‑dihydrouridine synthase B |
| RA | 3,452,057 | A→T | I77N (ATC→AAC) | rplD ← | 50S ribosomal subunit protein L4 |
| RA | 3,466,858 | G→C | A45G (GCC→GGC) | bfd ← | bacterioferritin‑associated ferredoxin |
| RA | 3,490,088 | A→G | G31G (GGT→GGC) | argD ← | bifunctional acetylornithine aminotransferase and succinyldiaminopimelate aminotransferase |
| RA | 3,540,351 | (A)6→5 | coding (189/228 nt) | feoA → | ferrous iron transporter, protein A |
| 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 | 3,574,062 | A→T | C273S (TGC→AGC) | asd ← | aspartate‑semialdehyde dehydrogenase, NAD(P)‑binding |
| RA | 3,582,272 | G→A | C137Y (TGT→TAT) | yhhZ → | putative Hcp1 family polymorphic toxin protein; putative colicin‑like DNase/tRNase activity |
| RA | 3,594,073 | G→T | T45N (ACC→AAC) | livG ← | branched‑chain amino acid ABC transporter ATPase |
| RA | 3,622,796 | T→G | L1202R (CTG→CGG) | rhsB → | Rhs protein with DUF4329 family putative toxin domain; putative neighboring cell growth inhibitor |
| RA | 3,636,979 | A→T | D144E (GAT→GAA) | yhiN ← | putative oxidoreductase |
| RA | 3,648,042 | T→C | intergenic (‑254/‑486) | dinQ ← / → arsR | UV‑inducible membrane toxin, DinQ‑AgrB type I toxin‑antitoxin system/arsenical resistance operon transcriptional repressor; autorepressor |
| RA | 3,678,937 | T→A | Q84L (CAG→CTG) | yhjH ← | cyclic‑di‑GMP phosphodiesterase, FlhDC‑regulated |
| RA | 3,704,719 | G→T | P15T (CCG→ACG) | dppC ← | dipeptide/heme ABC transporter permease |
| RA | 3,795,591 | G→A | S221S (TCG→TCA) | waaF → | ADP‑heptose:LPS heptosyltransferase II |
| RA | 3,799,324 | A→G | intergenic (‑12/+21) | waaU ← / ← waaZ | lipopolysaccharide core biosynthesis/lipopolysaccharide KdoIII transferase; lipopolysaccharide core biosynthesis protein |
| RA | 3,828,954 | T→C | S4P (TCC→CCC) | xanP → | xanthine permease |
| RA | 3,853,909 | A→G | intergenic (+267/‑13) | tisB → / → emrD | toxic membrane persister formation peptide, LexA‑regulated/multidrug efflux system protein |
| RA | 3,910,662 | A→T | D288E (GAT→GAA) | pstS ← | phosphate ABC transporter periplasmic binding protein |
| RA | 3,950,468 | G→T | intergenic (+48/‑39) | ilvL → / → ilvX | ilvG operon leader peptide/uncharacterized protein |
| RA | 3,971,690 | A→C | Q144P (CAG→CCG) | wecC → | UDP‑N‑acetyl‑D‑mannosaminuronic acid dehydrogenase |
| RA | 4,004,515 | G→C | G61G (GGC→GGG) | yigI ← | 4HBT thioesterase family protein |
| RA | 4,105,396 | A→T | L92Q (CTG→CAG) | cpxR ← | response regulator in two‑component regulatory system with CpxA |
| RA | 4,137,180 | C→G | A160P (GCA→CCA) | yijF ← | DUF1287 family protein |
| RA | 4,168,540 | T→A | intergenic (+93/‑101) | gltT → / → rrlB | tRNA‑Glu/23S ribosomal RNA of rrnB operon |
| RA | 4,235,689 | +A | intergenic (+282/‑217) | pgi → / → yjbE | glucosephosphate isomerase/extracellular polysaccharide production threonine‑rich protein |
| MC JC | 4,242,942 | Δ66 bp | coding (510‑575/891 nt) | malG ← | maltose transporter subunit |
| RA | 4,261,155 | A→T | D186V (GAT→GTT) | yjbM → | uncharacterized protein |
| RA | 4,296,381 | +GC | intergenic (+587/+55) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,490,055 | T→G | E3D (GAA→GAC) | yjgR ← | DUF853 family protein with NTPase fold |
| RA | 4,523,304 | G→T | P264H (CCT→CAT) | yjhG ← | putative dehydratase |
| RA | 4,544,598 | A→G | N99D (AAT→GAT) | fimC → | periplasmic chaperone |
| RA | 4,603,361 | A→G | intergenic (‑503/‑116) | yjjP ← / → yjjQ | DUF1212 family inner membrane protein/putative transcriptional regulator |
| RA | 4,615,859 | T→G | T403P (ACC→CCC) | yjjI ← | DUF3029 family protein, putative glycine radical enzyme |
| RA | 4,627,706 | T→G | F131C (TTT→TGT) | nadR → | trifunctional protein: nicotinamide mononucleotide adenylyltransferase, ribosylnicotinamide kinase, transcriptional repressor |
| RA | 4,631,700 | T→C | L323P (CTT→CCT) | slt → | lytic murein transglycosylase, soluble |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 3423720–3424234 | 3424574–3424238 | 5–855 | 43 [40] | [35] 41 | [rrfD]–[rrlD] | [rrfD], [rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 92 (1.150) | 63/190 | 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 | |||||
| * | ? | NC_000913 | = 1978502 | 0 (0.000) | 103 (1.340) | 74/182 | 0.0 | 100% | intergenic (‑305/+16) | flhD/insB1 | flagellar class II regulon transcriptional activator, with FlhC/IS1 transposase B |
| ? | NC_000913 | 1979279 = | 0 (0.000) | intergenic (‑64/‑474) | insA/uspC | IS1 repressor TnpA/universal stress protein | |||||