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 | 34,120 | (T)9→8 | intergenic (+82/‑180) | carB → / → caiF | carbamoyl phosphate synthetase subunit beta/DNA‑binding transcriptional activator CaiF |
| RA | 38,316 | T→C | H267R (CAT→CGT) | caiB ← | gamma‑butyrobetainyl‑CoA:carnitine CoA transferase |
| RA | 136,457 | (T)8→7 | coding (8/867 nt) | speE ← | spermidine synthase |
| RA | 139,009 | G→A | S739S (AGC→AGT) | gcd ← | quinoprotein glucose dehydrogenase |
| MC JC | 257,908 | Δ776 bp | insB9–[crl] | insB9, insA9, [crl] | |
| RA | 268,831 | Δ1 bp | coding (130/864 nt) | ykfA ← | CP4‑6 prophage; putative GTP‑binding protein YkfA |
| RA | 309,306 | T→C | G9G (GGA→GGG) | ecpC ← | putative fimbrial usher protein EcpC |
| RA | 340,298 | A→G | Y45C (TAC→TGC) | yahI → | carbamate kinase‑like protein YahI |
| RA | 380,022 | (G)10→9 | intergenic (‑141/+47) | frmR ← / ← yaiO | DNA‑binding transcriptional repressor FrmR/outer membrane protein YaiO |
| RA | 383,575 | A→G | Y121H (TAT→CAT) | yaiP ← | putative glucosyltransferase |
| RA | 476,580 | T→C | intergenic (+19/‑92) | ffs → / → ybaA | signal recognition particle 4.5S RNA/DUF1428 domain‑containing protein YbaA |
| RA | 486,373 | T→C | C205R (TGC→CGC) | acrR → | DNA‑binding transcriptional repressor AcrR |
| RA | 527,577 | T→C | intergenic (+36/‑4) | rhsD → / → ybbC | protein RhsD/PF15631 family protein YbbC |
| RA | 652,637 | T→C | F135L (TTC→CTC) | dpiB → | sensory histidine kinase DpiB |
| RA | 705,951 | T→A | intergenic (+61/‑142) | nagE → / → glnS | N‑acetylglucosamine specific PTS enzyme IIABC component/glutamine‑‑tRNA ligase |
| RA | 759,527 | (A)6→5 | coding (822/2802 nt) | sucA → | subunit of E1(0) component of 2‑oxoglutarate dehydrogenase |
| RA | 869,681 | A→G | K91E (AAA→GAA) | gsiB → | glutathione ABC transporter periplasmic binding protein |
| RA | 889,923 | A→G | intergenic (‑104/‑166) | ybjL ← / → ybjM | putative transport protein YbjL/putative inner membrane protein |
| RA | 890,825 | T→C | intergenic (‑72/‑88) | grxA ← / → ybjC | reduced glutaredoxin 1/DUF1418 domain‑containing protein YbjC |
| RA | 925,850 | (A)8→7 | intergenic (+310/+34) | clpA → / ← serW | ATP‑dependent Clp protease ATP‑binding subunit ClpA/tRNA‑Ser |
| RA | 932,340 | (A)8→7 | intergenic (‑290/‑255) | trxB ← / → lrp | thioredoxin reductase/DNA‑binding transcriptional dual regulator Lrp |
| RA | 949,055 | C→A | E172* (GAG→TAG) | ycaN ← | putative LysR‑type transcriptional regulator YcaN |
| RA | 981,850 | (G)6→5 | coding (804/1848 nt) | ldtD → | L,D‑transpeptidase LdtD |
| RA | 1,004,160 | (G)7→8 | coding (214/711 nt) | ycbF → | putative fimbrial chaperone YcbF |
| RA | 1,010,898 | C→T | A312V (GCC→GTC) | uup → | ATP‑binding protein with possible role in replication |
| RA | 1,022,327 | A→G | G519G (GGT→GGC) | yccS ← | putative transporter YccS |
| RA | 1,068,456 | A→G | intergenic (+202/+55) | ymdF → / ← rutG | conserved protein YmdF/pyrimidine:H(+) symporter |
| RA | 1,097,624 | T→C | noncoding (29/88 nt) | serX ← | tRNA‑Ser |
| RA | 1,143,140 | T→C | T410A (ACT→GCT) | rne ← | ribonuclease E |
| RA | 1,195,341 | (A)5→4 | coding (219/1251 nt) | icd → | isocitrate dehydrogenase |
| RA | 1,220,971 | G→A | pseudogene (1371/2648 nt) | ycgH → | putative transporter component, N‑terminal fragment |
| RA | 1,227,354 | T→C | Y40C (TAC→TGC) | pliG ← | inhibitor of g‑type lysozyme |
| RA | 1,236,278 | (G)6→7 | coding (964/1533 nt) | ycgB ← | PF04293 family protein YcgB |
| RA | 1,327,013 | Δ1 bp | coding (162/876 nt) | rluB → | 23S rRNA pseudouridine(2605) synthase |
| RA | 1,376,802 | G→A | A257T (GCC→ACC) | ycjR → | putative ketohexose‑3‑epimerase YcjR |
| RA | 1,388,633 | A→G | V60A (GTT→GCT) | tpx ← | lipid hydroperoxide peroxidase |
| RA | 1,390,505 | A→G | F32L (TTT→CTT) | mpaA ← | murein tripeptide amidase A |
| RA | 1,507,046 | A→G | Y89C (TAC→TGC) | rlhA → | 23S rRNA 5‑hydroxycytidine C2501 synthase |
| RA | 1,541,351 | C→T | E414K (GAA→AAA) | narZ ← | nitrate reductase Z subunit alpha |
| RA | 1,634,642 | C→T | G82S (GGC→AGC) | tfaQ ← | Qin prophage; putative tail fiber assembly protein TfaQ |
| RA | 1,659,283 | C→T | G405G (GGC→GGT) | ynfE → | putative selenate reductase YnfE |
| RA | 1,685,542 | (C)6→5 | coding (1047/1404 nt) | fumC ← | fumarase C |
| RA | 1,694,161 | A→G | Y35H (TAC→CAC) | uidB ← | glucuronide:H(+) symporter |
| RA | 1,706,044 | G→A | R93H (CGC→CAC) | rsxA → | SoxR [2Fe‑2S] reducing system protein RsxA |
| RA | 1,722,036 | T→C | V258A (GTT→GCT) | ydhJ → | putative membrane fusion protein YdhJ |
| RA | 1,771,070 | T→C | intergenic (+99/‑1) | ydiL → / → ydiM | DUF1870 domain‑containing protein YdiL/putative exporter YdiM |
| 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 | 1,886,426 | T→C | V194V (GTT→GTC) | yeaX → | carnitine monooxygenase subunit YeaX |
| RA | 1,888,023 | (A)8→9 | intergenic (‑32/+38) | rnd ← / ← fadD | RNase D/fatty acyl‑CoA synthetase |
| RA | 1,938,424 | A→G | D259G (GAC→GGC) | pykA → | pyruvate kinase II |
| MC JC | 1,978,503 | Δ776 bp | insB‑5–insA‑5 | insB‑5, insA‑5 | |
| RA | 2,049,210 | A→G | T1425A (ACC→GCC) | yeeJ → | inverse autotransporter adhesin |
| RA | 2,111,938 | A→G | G13G (GGT→GGC) | rfbD ← | dTDP‑4‑dehydrorhamnose reductase |
| RA | 2,139,033 | T→C | F378L (TTC→CTC) | yegH → | inner membrane protein YegH |
| RA | 2,143,684 | (G)6→7 | coding (419/3318 nt) | dgcE → | putative diguanylate cyclase DgcE |
| RA | 2,158,063 | A→G | N934S (AAC→AGC) | mdtB → | multidrug efflux pump RND permease subunit MdtB |
| RA | 2,173,363 | Δ2 bp | pseudogene (915‑916/1358 nt) | gatC ← | galactitol‑specific PTS enzyme IIC component |
| RA | 2,264,869 | G→A | G336D (GGT→GAT) | setB → | sugar exporter SetB |
| RA | 2,290,060 | T→C | R8G (AGA→GGA) | insH‑8 ← | IS5 transposase and trans‑activator |
| RA | 2,299,364 | A→G | L72P (CTG→CCG) | napH ← | ferredoxin‑type protein NapH |
| RA | 2,324,992 | G→A | P79P (CCG→CCA) | atoE → | short chain fatty acid transporter |
| RA | 2,445,924 | G→C | T154R (ACG→AGG) | mepA ← | peptidoglycan DD‑endopeptidase/peptidoglycan LD‑endopeptidase |
| RA | 2,446,579 | T→C | T299A (ACC→GCC) | aroC ← | chorismate synthase |
| RA | 2,462,889 | (C)9→10 | intergenic (+243/‑123) | fadL → / → yfdF | long‑chain fatty acid outer membrane channel/bacteriophage T2 receptor/protein YfdF |
| RA | 2,496,847 | C→T | intergenic (+282/‑74) | lpxP → / → ypdK | palmitoleoyl acyltransferase/putative membrane protein YpdK |
| RA | 2,504,395 | T→C | S31G (AGC→GGC) | fryA ← | putative PTS multiphosphoryl transfer protein FryA |
| RA | 2,527,823 | T→C | V293A (GTG→GCG) | yfeH → | putative solute:Na(+) symporter |
| RA | 2,528,944 | A→G | C411C (TGT→TGC) | ligA ← | DNA ligase |
| RA | 2,639,057 | (T)5→6 | coding (227/621 nt) | yfgM ← | ancillary SecYEG translocon subunit |
| RA | 2,682,157 | (C)7→8 | coding (589/3282 nt) | yphG ← | DUF5107 domain‑containing protein YphG |
| RA | 2,723,976 | A→G | H417R (CAC→CGC) | pssA → | phosphatidylserine synthase |
| JC | 2,765,463 | (TATGGCAC)6→9 | intergenic (‑310/+50) | abpA ← / ← yfjM | CP4‑57 prophage; anti‑bacteriophage protein/CP4‑57 prophage; protein YfjM |
| RA | 2,811,134 | A→G | H122R (CAC→CGC) | mprA → | DNA‑binding transcriptional repressor MprA |
| RA | 2,822,059 | T→C | intergenic (‑48/+80) | alaS ← / ← recX | alanine‑‑tRNA ligase/DNA‑binding transcriptional repressor/RecA inhibitor RecX |
| MC JC | 2,857,096 | Δ2,538 bp | coding (4‑2541/2562 nt) | mutS → | DNA mismatch repair protein MutS |
| RA | 2,870,249 | T→C | D9G (GAC→GGC) | umpG ← | broad specificity 5'(3')‑nucleotidase and polyphosphatase |
| RA | 2,875,210 | G→A | G70G (GGC→GGT) | cysN ← | sulfate adenylyltransferase subunit 1 |
| RA | 2,949,993 | (T)5→6 | coding (752/1332 nt) | argA → | N‑acetylglutamate synthase |
| RA | 2,957,099 | T→C | T596A (ACC→GCC) | ptrA ← | protease 3 |
| RA | 2,966,443 | A→G | D664D (GAT→GAC) | ptsP ← | phosphoenolpyruvate‑protein phosphotransferase PtsP |
| RA | 3,001,665 | T→C | Y441H (TAC→CAC) | xdhA → | putative xanthine dehydrogenase molybdenum‑binding subunit XdhA |
| RA | 3,027,458 | T→C | V113A (GTT→GCT) | ghxQ → | guanine/hypoxanthine transporter GhxQ |
| RA | 3,028,806 | (C)5→4 | coding (207/489 nt) | ygfS ← | putative oxidoreductase, 4Fe‑4S ferredoxin‑type subunit |
| RA | 3,056,598 | T→C | F120L (TTT→CTT) | fau → | putative 5‑formyltetrahydrofolate cyclo‑ligase |
| RA | 3,068,157 | T→C | intergenic (‑77/+16) | yggE ← / ← argO | uncharacterized protein YggE/L‑arginine exporter |
| RA | 3,091,961 | A→G | A28A (GCA→GCG) | gshB → | glutathione synthetase |
| RA | 3,097,116 | C→T | R146C (CGT→TGT) | rdgB → | dITP/XTP pyrophosphatase |
| RA | 3,101,039 | (C)7→8 | coding (585/720 nt) | yggN ← | putative EcfF |
| RA | 3,109,036 | A→G | A40A (GCT→GCC) | speC ← | ornithine decarboxylase, biosynthetic |
| RA | 3,121,739 | Δ1 bp | coding (2067/2172 nt) | glcB ← | malate synthase G |
| RA | 3,153,832 | Δ1 bp | coding (270/660 nt) | yghB → | DedA family protein YghB |
| RA | 3,166,883 | A→G | L279P (CTG→CCG) | ygiS ← | putative deoxycholate binding periplasmic protein |
| RA | 3,183,451 | T→C | D34G (GAC→GGC) | yqiD ← | protein YqiD |
| RA | 3,245,476 | T→C | W85R (TGG→CGG) | exuT → | hexuronate transporter |
| RA | 3,304,813 | (C)7→8 | coding (1005/1245 nt) | mtr ← | tryptophan:H(+) symporter Mtr |
| RA | 3,314,509 | T→C | K502K (AAA→AAG) | infB ← | translation initiation factor IF‑2 |
| RA | 3,332,445 | A→G | S97S (AGT→AGC) | yhbE ← | inner membrane protein YhbE |
| RA | 3,354,487 | C→T | intergenic (‑437/‑238) | yhcC ← / → gltB | radical SAM family oxidoreductase YhcC/glutamate synthase subunit GltB |
| RA | 3,377,917 | T→C | E97E (GAA→GAG) | rpsI ← | 30S ribosomal subunit protein S9 |
| RA | 3,388,726 | A→G | V134A (GTT→GCT) | aaeA ← | aromatic carboxylic acid efflux pump membrane fusion protein |
| RA | 3,419,982 | T→C | pseudogene (941/1025 nt) | yhdW → | putative ABC transporter periplasmic binding protein YhdW |
| RA | 3,432,994 | (C)6→7 | coding (567/1125 nt) | smf ← | protein Smf |
| RA | 3,560,455 | +G | pseudogene (151/758 nt) | glpR ← | DNA‑binding transcriptional repressor GlpR |
| RA | 3,572,091 | T→C | D471G (GAT→GGT) | glgB ← | 1,4‑alpha‑glucan branching enzyme |
| RA | 3,610,564 | (T)7→6 | coding (1170/1218 nt) | yhhS ← | putative transporter YhhS |
| RA | 3,622,367 | T→C | V1059A (GTC→GCC) | rhsB → | rhs element protein RhsB |
| RA | 3,650,599 | (A)5→4 | coding (363/426 nt) | arsC → | arsenate reductase |
| RA | 3,673,639 | (G)5→6 | coding (278/1014 nt) | yhjD → | putative transporter YhjD |
| RA | 3,709,561 | (C)6→5 | coding (915/1692 nt) | eptB ← | Kdo2‑lipid A phosphoethanolamine 7''‑transferase |
| RA | 3,711,960 | A→G | G16G (GGT→GGC) | yhjX ← | putative pyruvate transporter |
| RA | 3,779,515 | T→C | I154I (ATT→ATC) | lldR → | DNA‑binding transcriptional dual regulator LldR |
| RA | 3,781,054 | G→A | intergenic (+37/‑161) | lldD → / → trmL | L‑lactate dehydrogenase/tRNA (cytidine/uridine‑2'‑O)‑ribose methyltransferase |
| RA | 3,815,883 | +C | coding (667/687 nt) | rph ← | truncated RNase PH |
| RA | 3,860,630 | (C)5→4 | coding (348/894 nt) | yidL → | putative DNA‑binding transcriptional regulator YidL |
| RA | 3,869,040 | +G | coding (270/1248 nt) | yidR ← | DUF3748 domain‑containing galacturonate catabolism protein YidR |
| RA | 3,870,333 | T→C | R319R (CGT→CGC) | cbrA → | colicin M resistance protein |
| RA | 3,904,307 | T→C | S431G (AGC→GGC) | bglF ← | beta‑glucoside specific PTS enzyme II/BglG kinase/BglG phosphatase |
| RA | 3,974,495 | T→C | L10P (CTA→CCA) | rffC → | dTDP‑4‑amino‑4,6‑dideoxy‑D‑galactose acyltransferase |
| RA | 4,026,686 | A→G | T54A (ACG→GCG) | fre → | flavin reductase |
| RA | 4,142,585 | T→C | V19A (GTT→GCT) | frwC → | putative PTS enzyme IIC component FrwC |
| RA | 4,190,658 | (A)7→6 | intergenic (‑171/+77) | sroH ← / ← thiH | small RNA SroH/2‑iminoacetate synthase |
| RA | 4,238,397 | T→C | V255A (GTT→GCT) | yjbH → | YjbH family protein |
| RA | 4,296,381 | +GC | intergenic (+587/+55) | gltP → / ← yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| RA | 4,320,364 | A→G | R100R (CGT→CGC) | phnI ← | carbon‑phosphorus lyase core complex subunit PhnI |
| RA | 4,329,001 | C→T | P623S (CCC→TCC) | crfC → | clamp‑binding sister replication fork colocalization protein |
| RA | 4,341,014 | A→G | D205D (GAT→GAC) | melR ← | DNA‑binding transcriptional dual regulator MelR |
| RA | 4,386,805 | C→T | E856K (GAA→AAA) | mscM ← | miniconductance mechanosensitive channel MscM |
| RA | 4,387,080 | A→G | V764A (GTC→GCC) | mscM ← | miniconductance mechanosensitive channel MscM |
| RA | 4,410,053 | (T)9→8 | intergenic (+47/‑80) | rlmB → / → yjfI | 23S rRNA 2'‑O‑ribose G2251 methyltransferase/conserved protein YjfI |
| RA | 4,445,549 | A→G | T480A (ACC→GCC) | tamB → | translocation and assembly module subunit TamB |
| RA | 4,451,387 | A→G | E110E (GAA→GAG) | ytfR → | galactofuranose ABC transporter putative ATP binding subunit |
| RA | 4,509,987 | A→G | pseudogene (184/330 nt) | yjhV → | KpLE2 phage‑like element; putative uncharacterized protein YjhV |
| RA | 4,521,444 | A→G | L193L (TTG→CTG) | yjhF ← | KpLE2 phage‑like element; putative transporter YjhF |
| RA | 4,589,698 | (T)7→6 | coding (1582/2151 nt) | btsT ← | pyruvate:H(+) symporter |
| RA | 4,590,298 | A→G | F328L (TTC→CTC) | btsT ← | pyruvate:H(+) symporter |
| RA | 4,606,094 | (G)8→7 | noncoding (72/87 nt) | leuV ← | tRNA‑Leu |
| RA | 4,638,322 | A→G | T49A (ACC→GCC) | creD → | putative inner membrane protein |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 227083–228686 | 228907–228689 | 4–1825 | 30 [27] | [22] 34 | [rrlH]–rrfH | [rrlH],rrfH |
| * | * | ÷ | NC_000913 | 3423758–3424234 | 3424538–3424238 | 5–781 | 28 [27] | [27] 31 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 1207790 = | 80 (0.890) | 48 (0.600) | 36/244 | 1.0 | 45.6% | coding (290/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | 1209619 = | 44 (0.550) | pseudogene (37/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 1207805 | 80 (0.890) | 35 (0.440) | 31/244 | 1.4 | 37.9% | coding (305/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | = 1209602 | 44 (0.550) | pseudogene (54/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 87 (0.990) | 53/268 | 0.4 | 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 = | 123 (1.360) | 104 (1.160) | 62/274 | 0.2 | 62.8% | coding (195/2382 nt) | yhcD | putative fimbrial usher protein YhcD |
| ? | NC_000913 | 3766087 = | 1 (0.010) | coding (3905/4134 nt) | rhsA | rhs element protein RhsA | |||||
| * | ? | NC_000913 | = 3653230 | NA (NA) | 87 (0.960) | 57/276 | 0.3 | 98.9% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 3766089 | 1 (0.010) | coding (3907/4134 nt) | rhsA | rhs element protein RhsA | |||||