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 | 222,731 | C→T | intergenic (‑86/‑102) | metN ← / → gmhB | DL‑methionine transporter subunit/D,D‑heptose 1,7‑bisphosphate phosphatase |
| RA | 236,541 | C→T | R159* (CGA→TGA) | dnaQ → | DNA polymerase III epsilon subunit |
| MC JC | 257,908 | Δ776 bp | [crl] | [crl] | |
| RA | 343,467 | A→C | H195P (CAC→CCC) | yahK → | broad specificity NADPH‑dependent aldehyde reductase, Zn‑containing |
| RA | 409,322 | G→T | A233E (GCG→GAG) | rdgC ← | nucleoid‑associated ssDNA and dsDNA binding protein; competitive inhibitor of RecA function |
| 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 | 548,374 | G→A | A6A (GCG→GCA) | ylbE → | NO‑induced DUF1116 protein |
| RA | 575,915 | T→A | pseudogene (911/1040 nt) | nmpC ← | DLP12 prophage; truncated outer membrane porin (pseudogene);IS, phage, Tn; Phage or Prophage Related; outer membrane porin protein; locus of qsr prophage |
| RA | 580,851 | G→A | K6K (AAG→AAA) | nohD → | DLP12 prophage; DNA packaging protein |
| RA | 674,180 | G→A | L202L (CTG→TTG) | leuS ← | leucyl‑tRNA synthetase |
| RA | 700,805 | A→T | C264S (TGC→AGC) | nagC ← | N‑acetylglucosamine‑inducible nag divergent operon transcriptional repressor |
| RA | 710,882 | +T | intergenic (‑157/+53) | uof ← / ← fldA | ryhB‑regulated fur leader peptide/flavodoxin 1 |
| RA | 720,946 | C→T | intergenic (+106/+110) | ybfK → / ← kdpE | uncharacterized protein/response regulator in two‑component regulatory system with KdpD |
| RA | 755,789 | G→A | W77* (TGG→TAG) | sdhD → | succinate dehydrogenase, membrane subunit, binds cytochrome b556 |
| RA | 772,209 | C→A | T251N (ACC→AAC) | cydA → | cytochrome d terminal oxidase, subunit I |
| RA | 843,368 | (T)6→5 | coding (2113/2226 nt) | ybiO ← | mechanosensitive channel protein, intermediate conductance |
| RA | 850,742 | A→G | D98G (GAC→GGC) | ompX → | outer membrane protein X |
| RA | 882,722 | G→A | R5C (CGC→TGC) | deoR ← | deoxyribose‑5‑phosphate‑inducible deoxyribose operon transcriptional repressor; repressor of nupG and tsx |
| RA | 894,155 | T→G | D124E (GAT→GAG) | potF → | putrescine ABC transporter periplasmic binding protein |
| RA | 1,031,761 | T→C | intergenic (‑49/‑378) | serT ← / → hyaA | tRNA‑Ser/hydrogenase 1, small subunit |
| RA | 1,080,039 | (G)5→4 | coding (735/1509 nt) | 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 | 1,172,553 | A→G | I471T (ATC→ACC) | mfd ← | transcription‑repair coupling factor |
| RA | 1,197,739 | A→G | S167P (TCC→CCC) | ymfE ← | e14 prophage; putative inner membrane protein |
| RA | 1,212,319 | (T)5→4 | intergenic (‑316/+384) | iraM ← / ← ycgX | RpoS stabilzer during Mg starvation, anti‑RssB factor/DUF1398 family protein |
| RA | 1,219,033 | C→T | S17S (TCC→TCT) | ymgF → | inner membrane division septum protein |
| RA | 1,254,980 | A→G | F325L (TTT→CTT) | ycgV ← | putative adhesin |
| RA | 1,292,944 | T→C | intergenic (‑22/‑583) | hns ← / → tdk | global DNA‑binding transcriptional dual regulator H‑NS/thymidine kinase/deoxyuridine kinase |
| RA | 1,325,850 | C→T | R369C (CGC→TGC) | yciQ → | enhancer of membrane protein expression; putative inner membrane protein |
| RA | 1,401,844 | A→G | I471T (ATC→ACC) | abgB ← | p‑aminobenzoyl‑glutamate hydrolase, B subunit |
| RA | 1,417,290 | A→T | C33S (TGT→AGT) | recE ← | Rac prophage; exonuclease VIII, 5' to 3' specific dsDNA exonuclease |
| 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 | 1,501,912 | T→A | I117I (ATT→ATA) | tehB → | tellurite, selenium methyltransferase, SAM‑dependent; tellurite, selenium resistance protein |
| 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 | 1,665,195 | (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 | 1,728,444 | C→A | T33N (ACC→AAC) | rnt → | RNase T; exoribonuclease T; structured DNA 3' exonuclease; RNA processing; DNA repair |
| RA | 1,827,031 | T→A | D410V (GAT→GTT) | astB ← | succinylarginine dihydrolase |
| MC JC | 1,978,503 | Δ776 bp | insB1–insA | insB1, insA | |
| RA | 1,983,761 | C→T | E437K (GAA→AAA) | araG ← | L‑arabinose ABC transporter ATPase |
| RA | 2,062,022 | A→C | intergenic (‑89/‑238) | nac ← / → asnV | nitrogen assimilation regulon transcriptional regulator; autorepressor/tRNA‑Asn |
| 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 | 2,225,612 | A→T | L7Q (CTG→CAG) | yohC ← | Yip1 family inner membrane protein |
| RA | 2,278,298 | C→T | intergenic (‑61/+272) | yejG ← / ← bcr | uncharacterized protein/bicyclomycin/cysteine/sulfonamide efflux transporter |
| RA | 2,291,084 | A→C | K195N (AAA→AAC) | narP → | response regulator in two‑component regulatory system with NarQ |
| RA | 2,352,993 | T→A | I116N (ATC→AAC) | glpA → | anaerobic sn‑glycerol‑3‑phosphate dehydrogenase, large FAD/NAD(P)‑binding subunit |
| RA | 2,436,937 | A→T | D305E (GAT→GAA) | pdxB ← | erythronate‑4‑phosphate dehydrogenase |
| RA | 2,452,339 | A→G | intergenic (‑3/+17) | yfcS ← / ← yfcU | putative periplasmic pilin chaperone/pseudogene, FimD fimbrial export usher family;putative membrane; Not classified; putative outer membrane protein |
| RA | 2,469,656 | (T)7→8 | coding (526/1332 nt) | gtrS → | serotype‑specific glucosyl transferase, CPS‑53 (KpLE1) prophage |
| 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 | 2,712,402 | A→G | S121S (AGT→AGC) | trmN ← | tRNA1(Val) (adenine(37)‑N6)‑methyltransferase |
| RA | 2,782,883 | G→A | intergenic (‑157/+182) | ypjA ← / ← pinH | adhesin‑like autotransporter/pseudogene, invertase resolvase family |
| 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 | 2,852,356 | T→A | L74Q (CTG→CAG) | hypD → | hydrogenase maturation protein |
| RA | 2,867,151 | A→G | F134S (TTT→TCT) | rpoS ← | RNA polymerase, sigma S (sigma 38) factor |
| 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 | 2,989,886 | T→A | D5V (GAT→GTT) | yqeL ← | uncharacterized protein |
| RA | 3,218,198 | C→T | Q293Q (CAG→CAA) | aer ← | fused signal transducer for aerotaxis sensory component/methyl accepting chemotaxis component |
| RA | 3,452,057 | A→T | I77N (ATC→AAC) | rplD ← | 50S ribosomal subunit protein L4 |
| RA | 3,540,239 | T→A | L26Q (CTG→CAG) | 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 | 3,595,057 | A→C | Y142D (TAC→GAC) | livM ← | branched‑chain amino acid ABC transporter permease |
| RA | 3,622,796 | T→G | L1202R (CTG→CGG) | rhsB → | Rhs protein with DUF4329 family putative toxin domain; putative neighboring cell growth inhibitor |
| RA | 3,648,042 | 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 | 3,736,609 | G→A | P190L (CCA→CTA) | bax ← | putative glucosaminidase |
| RA | 3,853,312 | T→C | intergenic (‑324/‑241) | ivbL ← / → tisB | ilvB operon leader peptide/toxic membrane persister formation peptide, LexA‑regulated |
| RA | 3,853,909 | A→G | intergenic (+267/‑13) | tisB → / → emrD | toxic membrane persister formation peptide, LexA‑regulated/multidrug efflux system protein |
| RA | 3,881,837 | G→T | T162N (ACC→AAC) | dnaN ← | DNA polymerase III, beta subunit |
| RA | 3,910,662 | A→T | D288E (GAT→GAA) | pstS ← | phosphate ABC transporter periplasmic binding protein |
| RA | 3,910,707 | A→T | D273E (GAT→GAA) | pstS ← | phosphate ABC transporter periplasmic binding protein |
| RA | 3,950,467 | 2 bp→TT | intergenic (+47/‑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 | 4,168,540 | 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 | 4,296,381 | +GC | intergenic (+587/+55) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,324,454 | G→T | Q238K (CAA→AAA) | phnC ← | phosphonate ABC transporter ATPase |
| RA | 4,434,437 | T→A | W109R (TGG→AGG) | ytfH → | DUF24 family HxlR‑type putative transcriptional regulator |
| RA | 4,490,055 | T→G | E3D (GAA→GAC) | yjgR ← | DUF853 family protein with NTPase fold |
| RA | 4,560,045 | C→A | W212C (TGG→TGT) | yjiH ← | nucleoside recognition pore and gate family putative inner membrane transporter |
| RA | 4,568,688 | C→A | intergenic (‑169/‑310) | mdtM ← / → yjiP | multidrug efflux system protein/pseudogene, transposase_31 family protein |
| RA | 4,615,859 | T→G | T403P (ACC→CCC) | yjjI ← | DUF3029 family protein, putative glycine radical enzyme |
| 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 | 3423722–3424234 | 3424593–3424238 | 5–872 | 30 [29] | [28] 31 | [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) | 71 (1.150) | 60/190 | 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 | |||||