mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.35.4 revision f352f80f4bc9
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Predicted mutations | |||||
|---|---|---|---|---|---|
| evidence | position | mutation | annotation | gene | description |
| RA | 310 | (T)9→8 | intergenic (+55/‑27) | thrL → / → thrA | thr operon leader peptide/fused aspartate kinase/homoserine dehydrogenase 1 |
| RA | 18,694 | Δ1 bp | intergenic (+39/‑21) | nhaA → / → nhaR | Na(+):H(+) antiporter NhaA/DNA‑binding transcriptional activator NhaR |
| RA | 47,000 | T→C | G398G (GGT→GGC) | yaaU → | putative transporter YaaU |
| RA | 62,766 | G→A | R167C (CGC→TGC) | rapA ← | RNA polymerase‑binding ATPase and RNAP recycling factor |
| RA | 93,243 | A→G | T26T (ACA→ACG) | murE → | UDP‑N‑acetylmuramoyl‑L‑alanyl‑D‑glutamate‑‑2, 6‑diaminopimelate ligase |
| RA | 110,714 | A→G | A812A (GCA→GCG) | secA → | protein translocation ATPase |
| RA | 123,000 | T→C | intergenic (+144/‑17) | pdhR → / → aceE | DNA‑binding transcriptional dual regulator PdhR/pyruvate dehydrogenase E1 component |
| RA | 200,441 | A→G | intergenic (+81/‑41) | bamA → / → skp | outer membrane protein assembly factor BamA/periplasmic chaperone Skp |
| MC JC | 257,908 | Δ776 bp | insB9–[crl] | insB9, insA9, [crl] | |
| RA | 321,564 | (G)7→8 | intergenic (+483/‑44) | rclR → / → ykgE | DNA‑binding transcriptional activator RclR/putative lactate utilization oxidoreductase YkgE |
| RA | 372,753 | C→T | R213R (CGC→CGT) | mhpD → | 2‑hydroxypentadienoate hydratase |
| RA | 380,022 | (G)10→9 | intergenic (‑141/+47) | frmR ← / ← yaiO | DNA‑binding transcriptional repressor FrmR/outer membrane protein YaiO |
| RA | 398,192 | C→T | D107D (GAC→GAT) | yaiW → | surface‑exposed outer membrane lipoprotein |
| RA | 402,089 | (A)7→8 | coding (343/1416 nt) | phoA → | alkaline phosphatase |
| RA | 465,107 | A→G | S147S (AGT→AGC) | queC ← | 7‑cyano‑7‑deazaguanine synthase |
| RA | 481,357 | A→G | V1016A (GTA→GCA) | acrB ← | multidrug efflux pump RND permease AcrB |
| RA | 482,378 | T→C | T676A (ACT→GCT) | acrB ← | multidrug efflux pump RND permease AcrB |
| RA | 527,577 | T→C | intergenic (+36/‑4) | rhsD → / → ybbC | protein RhsD/PF15631 family protein YbbC |
| RA | 534,735 | G→C | V274L (GTG→CTG) | gcl → | glyoxylate carboligase |
| RA | 560,984 | A→G | T430A (ACG→GCG) | sfmD → | putative fimbrial usher protein SfmD |
| RA | 639,292 | T→C | G116G (GGT→GGC) | ahpC → | alkyl hydroperoxide reductase, AhpC component |
| RA | 697,118 | A→G | noncoding (16/77 nt) | metT ← | tRNA‑Met |
| RA | 717,802 | (C)6→7 | coding (464/1320 nt) | potE ← | putrescine:H(+) symporter/putrescine:ornithine antiporter PotE |
| RA | 766,957 | (G)6→7 | coding (974/1977 nt) | mngA → | 2‑O‑alpha‑mannosyl‑D‑glycerate specific PTS enzyme II |
| RA | 772,290 | A→G | E278G (GAA→GGA) | cydA → | cytochrome bd‑I ubiquinol oxidase subunit I |
| RA | 838,326 | (G)5→4 | coding (131/267 nt) | ybiI ← | zinc finger domain‑containing protein YbiI |
| RA | 883,178 | A→G | S71P (TCC→CCC) | ybjG ← | undecaprenyl pyrophosphate phosphatase |
| RA | 889,923 | A→G | intergenic (‑104/‑166) | ybjL ← / → ybjM | putative transport protein YbjL/putative inner membrane protein |
| RA | 893,874 | (A)6→7 | coding (91/1113 nt) | potF → | putrescine ABC transporter periplasmic binding protein |
| RA | 913,473 | C→T | P114P (CCG→CCA) | hcp ← | protein S‑nitrosylase |
| RA | 932,340 | (A)8→7 | intergenic (‑290/‑255) | trxB ← / → lrp | thioredoxin reductase/DNA‑binding transcriptional dual regulator Lrp |
| RA | 967,775 | C→T | I385I (ATC→ATT) | msbA → | ATP‑binding lipopolysaccharide transport protein |
| RA | 1,008,117 | G→A | A92T (GCT→ACT) | rlmL → | fused 23S rRNA m(2)G2445 methyltransferase and 23S rRNA m(7)G2069 methyltransferase |
| RA | 1,010,898 | C→T | A312V (GCC→GTC) | uup → | ATP‑binding protein with possible role in replication |
| RA | 1,040,609 | A→G | intergenic (+72/‑8) | appX → / → appA | small protein AppX/periplasmic phosphoanhydride phosphatase/multiple inositol‑polyphosphate phosphatase |
| RA | 1,067,364 | A→G | G115G (GGT→GGC) | wrbA ← | NAD(P)H:quinone oxidoreductase |
| RA | 1,105,562 | C→T | P50L (CCC→CTC) | ymdA → | uncharacterized protein YmdA |
| RA | 1,122,056 | A→G | A184A (GCT→GCC) | pyrC ← | dihydroorotase |
| RA | 1,124,109 | A→G | intergenic (‑55/+9) | grxB ← / ← mdtH | reduced glutaredoxin 2/multidrug efflux pump MdtH |
| RA | 1,143,140 | T→C | T410A (ACT→GCT) | rne ← | ribonuclease E |
| RA | 1,173,437 | A→G | S176S (AGT→AGC) | mfd ← | transcription‑repair coupling factor |
| RA | 1,216,120 | T→C | V18A (GTG→GCG) | ymgA → | putative two‑component system connector protein YmgA |
| RA | 1,220,971 | G→A | pseudogene (1371/2648 nt) | ycgH → | putative transporter component, N‑terminal fragment |
| RA | 1,264,239 | A→G | I176V (ATC→GTC) | hemA → | glutamyl‑tRNA reductase |
| RA | 1,399,763 | T→C | R158R (CGA→CGG) | ogt ← | methylated‑DNA‑‑[protein]‑cysteine S‑methyltransferase |
| RA | 1,437,231 | (T)9→8 | intergenic (+2/+29) | micC → / ← ydbK | small regulatory RNA MicC/putative pyruvate‑flavodoxin oxidoreductase |
| RA | 1,474,315 | (C)6→5 | coding (95/861 nt) | pdxI → | pyridoxine 4‑dehydrogenase |
| RA | 1,484,109 | T→C | V350A (GTC→GCC) | hrpA → | ATP‑dependent RNA helicase HrpA |
| RA | 1,508,221 | (G)5→4 | coding (1441/1962 nt) | rlhA → | 23S rRNA 5‑hydroxycytidine C2501 synthase |
| RA | 1,541,351 | C→T | E414K (GAA→AAA) | narZ ← | nitrate reductase Z subunit alpha |
| RA | 1,585,101 | (C)6→7 | coding (1386/2280 nt) | ydeP ← | putative oxidoreductase YdeP |
| RA | 1,593,081 | T→C | pseudogene (5006/5422 nt) | yneO ← | AIDA‑I family autotransporter YneO |
| RA | 1,594,256 | (C)8→9 | pseudogene (3831/5422 nt) | yneO ← | AIDA‑I family autotransporter YneO |
| RA | 1,634,642 | C→T | G82S (GGC→AGC) | tfaQ ← | Qin prophage; putative tail fiber assembly protein TfaQ |
| RA | 1,685,542 | (C)6→5 | coding (1047/1404 nt) | fumC ← | fumarase C |
| RA | 1,714,326 | (T)9→8 | intergenic (+55/‑51) | dtpA → / → gstA | dipeptide/tripeptide:H(+) symporter DtpA/glutathione S‑transferase GstA |
| RA | 1,731,481 | A→G | T799A (ACC→GCC) | lhr → | putative ATP‑dependent helicase Lhr |
| RA | 1,756,033 | T→C | G112G (GGT→GGC) | pykF → | pyruvate kinase I |
| RA | 1,770,856 | (T)6→5 | coding (242/357 nt) | ydiL → | DUF1870 domain‑containing protein YdiL |
| RA | 1,812,902 | A→G | S77S (AGT→AGC) | ydjO ← | protein YdjO |
| RA | 1,853,538 | A→G | S148P (TCC→CCC) | ydjE ← | putative transporter YdjE |
| RA | 1,860,778 | T→C | P185P (CCA→CCG) | ydjL ← | putative zinc‑binding dehydrogenase YdjL |
| RA | 1,873,384 | A→G | K448K (AAA→AAG) | dgcJ → | putative diguanylate cyclase DgcJ |
| JC JC | 1,879,829 | Δ1 bp :: IS186 (–) +6 bp :: Δ1 bp | coding (115‑120/360 nt) | yeaR ← | DUF1971 domain‑containing protein YeaR |
| RA | 1,951,064 | T→C | V78A (GTG→GCG) | yecD → | putative hydrolase |
| MC JC | 1,978,503 | Δ776 bp | insB‑5–insA‑5 | insB‑5, insA‑5 | |
| RA | 2,037,372 | T→C | T261A (ACG→GCG) | hprS ← | sensory histidine kinase HprS |
| RA | 2,117,430 | (C)5→6 | coding (975/1281 nt) | wcaK ← | putative colanic acid biosynthesis pyruvyl transferase |
| RA | 2,173,363 | Δ2 bp | pseudogene (915‑916/1358 nt) | gatC ← | galactitol‑specific PTS enzyme IIC component |
| RA | 2,214,339 | (C)6→5 | coding (306/1686 nt) | btsS ← | high‑affinity pyruvate receptor |
| RA | 2,236,484 | A→G | H407R (CAC→CGC) | preA → | NAD‑dependent dihydropyrimidine dehydrogenase subunit PreA |
| RA | 2,258,312 | T→C | D19G (GAC→GGC) | psuG ← | pseudouridine‑5'‑phosphate glycosidase |
| RA | 2,267,029 | T→C | V262A (GTG→GCG) | yeiQ → | putative dehydrogenase, NAD‑dependent |
| RA | 2,277,598 | T→C | R433R (CGT→CGC) | yejF → | putative oligopeptide ABC transporter ATP binding subunit |
| RA | 2,287,208 | T→C | pseudogene (1707/2525 nt) | yejO ← | adhesin‑like autotransporter YejO |
| RA | 2,312,636 | T→C | V38V (GTA→GTG) | ompC ← | outer membrane porin C |
| RA | 2,331,613 | A→G | pseudogene (2790/4605 nt) | yfaS ← | putative macroglobulin family protein, N‑terminal fragment |
| RA | 2,339,991 | T→C | V142A (GTC→GCC) | ubiG → | bifunctional 3‑demethylubiquinone‑8 3‑O‑methyltransferase and 2‑octaprenyl‑6‑hydroxyphenol methylase |
| RA | 2,411,136 | T→C | T73A (ACC→GCC) | yfbS ← | putative transporter YfbS |
| RA | 2,446,579 | T→C | T299A (ACC→GCC) | aroC ← | chorismate synthase |
| RA | 2,527,823 | T→C | V293A (GTG→GCG) | yfeH → | putative solute:Na(+) symporter |
| RA | 2,577,609 | C→T | A257T (GCG→ACG) | maeB ← | malate dehydrogenase |
| RA | 2,604,329 | T→C | G161G (GGT→GGC) | hyfC → | hydrogenase 4 component C |
| RA | 2,613,047 | T→C | V383A (GTG→GCG) | hyfR → | DNA‑binding transcriptional activator HyfR |
| RA | 2,623,014 | T→C | intergenic (+142/‑30) | purN → / → ppk | phosphoribosylglycinamide formyltransferase 1/polyphosphate kinase |
| RA | 2,628,895 | (C)5→4 | coding (44/2244 nt) | pdeF ← | cyclic di‑GMP phosphodiesterase PdeF |
| RA | 2,668,030 | T→C | E14E (GAA→GAG) E289E (GAA→GAG) |
iroK ← hcaR ← |
protein IroK DNA‑binding transcriptional dual regulator HcaR |
| RA | 2,811,134 | A→G | H122R (CAC→CGC) | mprA → | DNA‑binding transcriptional repressor MprA |
| MC JC | 2,857,096 | Δ2,538 bp | coding (4‑2541/2562 nt) | mutS → | DNA mismatch repair protein MutS |
| RA | 2,886,788 | A→T | H144Q (CAT→CAA) | cas3 ← | CRISPR‑associated endonuclease/helicase Cas3 |
| RA | 2,911,717 | G→T | R645R (CGC→CGA) | relA ← | GDP/GTP pyrophosphokinase |
| RA | 2,949,993 | (T)5→6 | coding (752/1332 nt) | argA → | N‑acetylglutamate synthase |
| RA | 2,953,848 | T→C | D719G (GAC→GGC) | recB ← | exodeoxyribonuclease V subunit RecB |
| RA | 2,967,016 | G→A | F473F (TTC→TTT) | ptsP ← | phosphoenolpyruvate‑protein phosphotransferase PtsP |
| RA | 3,000,660 | Δ1 bp | coding (316/2259 nt) | xdhA → | putative xanthine dehydrogenase molybdenum‑binding subunit XdhA |
| RA | 3,031,909 | T→C | N181N (AAT→AAC) | uacT → | urate:H(+) symporter |
| RA | 3,068,157 | T→C | intergenic (‑77/+16) | yggE ← / ← argO | uncharacterized protein YggE/L‑arginine exporter |
| RA | 3,080,454 | T→C | K394K (AAA→AAG) | tktA ← | transketolase 1 |
| RA | 3,088,177 | T→C | intergenic (+317/‑107) | metK → / → galP | methionine adenosyltransferase/galactose:H(+) symporter |
| RA | 3,220,860 | T→C | V456A (GTC→GCC) | patA → | putrescine aminotransferase |
| RA | 3,240,079 | T→C | L46L (TTA→CTA) | sstT → | serine/threonine:Na(+) symporter |
| RA | 3,246,199 | T→C | Y326H (TAT→CAT) | exuT → | hexuronate transporter |
| RA | 3,354,487 | C→T | intergenic (‑437/‑238) | yhcC ← / → gltB | radical SAM family oxidoreductase YhcC/glutamate synthase subunit GltB |
| RA | 3,379,381 | T→C | N206S (AAC→AGC) | zapE ← | cell division factor ZapE with ATPase activity |
| RA | 3,388,726 | A→G | V134A (GTT→GCT) | aaeA ← | aromatic carboxylic acid efflux pump membrane fusion protein |
| RA | 3,411,831 | T→C | L60P (CTG→CCG) | yhdJ → | DNA adenine methyltransferase |
| RA | 3,471,633 | T→C | T628A (ACC→GCC) | fusA ← | elongation factor G |
| RA | 3,476,531 | T→C | intergenic (‑91/+76) | yheO ← / ← fkpA | putative DNA‑binding transcriptional regulator YheO/peptidyl‑prolyl cis‑trans isomerase FkpA |
| RA | 3,489,724 | Δ1 bp | coding (457/1221 nt) | argD ← | N‑acetylornithine aminotransferase/N‑succinyldiaminopimelate aminotransferase |
| RA | 3,560,455 | +G | pseudogene (151/758 nt) | glpR ← | DNA‑binding transcriptional repressor GlpR |
| RA | 3,579,480 | T→C | T56A (ACT→GCT) | yhhW ← | quercetin 2,3‑dioxygenase |
| RA | 3,579,816 | T→C | E330E (GAA→GAG) | yhhX ← | putative oxidoreductase YhhX |
| RA | 3,624,198 | T→C | intergenic (+416/‑180) | yhhH → / → yhhI | PF15631 family protein YhhH/putative transposase |
| RA | 3,626,245 | T→C | T187A (ACC→GCC) | yhhJ ← | ABC transporter family protein YhhJ |
| RA | 3,720,192 | T→C | G48G (GGT→GGC) | cspA → | cold shock protein CspA |
| RA | 3,781,338 | A→G | K42E (AAG→GAG) | trmL → | tRNA (cytidine/uridine‑2'‑O)‑ribose methyltransferase |
| RA | 3,785,021 | (G)6→7 | intergenic (‑6/‑239) | yibN ← / → gpmM | putative sulfurtransferase YibN/2,3‑bisphosphoglycerate‑independent phosphoglycerate mutase |
| RA | 3,815,883 | +C | coding (667/687 nt) | rph ← | truncated RNase PH |
| RA | 3,859,535 | A→G | G194G (GGT→GGC) | yidK ← | putative transporter YidK |
| RA | 3,860,630 | (C)5→4 | coding (348/894 nt) | yidL → | putative DNA‑binding transcriptional regulator YidL |
| RA | 3,902,262 | T→C | intergenic (‑42/+27) | bglH ← / ← bglB | carbohydrate‑specific outer membrane porin, cryptic/6‑phospho‑beta‑glucosidase B |
| RA | 3,998,395 | C→T | P138L (CCG→CTG) | uvrD → | ssDNA translocase and dsDNA helicase ‑ DNA helicase II |
| RA | 4,001,107 | T→C | intergenic (‑51/‑319) | yigE ← / → corA | DUF2233 domain‑containing protein YigE/Ni(2(+))/Co(2(+))/Mg(2(+)) transporter |
| RA | 4,134,855 | A→G | T341A (ACC→GCC) | katG → | hydroperoxidase I |
| RA | 4,151,314 | C→T | A595A (GCG→GCA) | ppc ← | phosphoenolpyruvate carboxylase |
| RA | 4,168,396 | A→G | noncoding (25/76 nt) | gltT → | tRNA‑Glu |
| RA | 4,296,381 | +GC | intergenic (+587/+55) | gltP → / ← yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| RA | 4,300,353 | C→T | A226A (GCG→GCA) | mdtP ← | putative multidrug efflux pump outer membrane channel |
| RA | 4,323,211 | Δ1 bp | pseudogene (71/839 nt) | phnE ← | phosphonate ABC transporter membrane subunit |
| RA | 4,368,924 | A→G | L87L (TTA→TTG) | fxsA → | protein FxsA |
| RA | 4,382,831 | C→T | P63P (CCC→CCT) | epmA → | EF‑P‑lysine lysyltransferase |
| RA | 4,399,710 | T→A | D153E (GAT→GAA) | miaA → | tRNA dimethylallyltransferase |
| RA | 4,417,594 | A→G | T215A (ACG→GCG) | yjfP → | carboxylesterase |
| RA | 4,445,549 | A→G | T480A (ACC→GCC) | tamB → | translocation and assembly module subunit TamB |
| RA | 4,448,836 | G→C | A49P (GCC→CCC) | chpB → | endoribonuclease toxin ChpB |
| RA | 4,512,215 | A→G | V67A (GTG→GCG) | fecD ← | ferric citrate ABC transporter membrane subunit FecD |
| RA | 4,546,947 | A→G | S618G (AGT→GGT) | fimD → | type I fimbriae usher protein |
| RA | 4,606,330 | (G)8→7 | noncoding (72/87 nt) | leuQ ← | tRNA‑Leu |
| RA | 4,616,640 | T→C | I142M (ATA→ATG) | yjjI ← | DUF3029 domain‑containing protein YjjI |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 1433321–1433371 | 1434232–1434076 | 706–912 | 17 [16] | [16] 20 | [pinR]–ynaE | [pinR],ynaE |
| * | * | ÷ | NC_000913 | 1570762–1570865 | 1571697–1571405 | 541–936 | 17 [15] | [16] 17 | gadB | glutamate decarboxylase B |
| * | * | ÷ | NC_000913 | 2066574–2066706 | 2067187–2066726 | 21–614 | 17 [16] | [16] 20 | insH‑6 | CP4‑44 prophage; IS5 transposase and trans‑activator |
| * | * | ÷ | NC_000913 | 3423770–3424233 | 3424525–3424238 | 6–756 | 17 [14] | [12] 18 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| * | * | ÷ | NC_000913 | 3944166–3945567 | 3946106–3945569 | 3–1941 | 17 [16] | [16] 17 | rrlC | 23S ribosomal RNA |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 1207790 = | 97 (1.430) | 17 (0.280) | 14/244 | 2.6 | 21.2% | coding (290/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | 1209619 = | 41 (0.680) | pseudogene (37/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 75 (1.140) | 47/268 | 0.2 | 100% | intergenic (+253/‑33) | ychE/insH21 | putative inner membrane protein/IS5 transposase and trans‑activator |
| ? | NC_000913 | 1300698 = | 0 (0.000) | intergenic (+151/‑484) | insH21/oppA | IS5 transposase and trans‑activator/oligopeptide ABC transporter periplasmic binding protein | |||||
| * | ? | NC_000913 | 3363001 = | 90 (1.320) | 91 (1.350) | 58/274 | 0.1 | 66.6% | coding (195/2382 nt) | yhcD | putative fimbrial usher protein YhcD |
| ? | NC_000913 | 3766087 = | 2 (0.030) | coding (3905/4134 nt) | rhsA | rhs element protein RhsA | |||||
| * | ? | NC_000913 | = 3653230 | NA (NA) | 65 (0.960) | 41/276 | 0.5 | 100% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 3766089 | 0 (0.000) | coding (3907/4134 nt) | rhsA | rhs element protein RhsA | |||||
| * | ? | NC_000913 | 4542682 = | 44 (0.650) | 26 (0.410) | 21/258 | 1.7 | 35.4% | intergenic (+49/‑433) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | 4542996 = | 54 (0.850) | intergenic (+363/‑119) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | = 4542690 | 44 (0.650) | 17 (0.270) | 15/258 | 2.6 | 26.3% | intergenic (+57/‑425) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | = 4542986 | 54 (0.850) | intergenic (+353/‑129) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||