mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.39.0
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Predicted mutations | |||||
|---|---|---|---|---|---|
| evidence | position | mutation | annotation | gene | description |
| MC JC | 257,908 | Δ776 bp | insB9–[crl] | insB9, insA9, [crl] | |
| MC JC | 275,150 | Δ17,303 bp | IS5‑mediated | mmuP–[yagK] | 19 genes mmuP, mmuM, afuC, insB2, insA2, yagB, yagA, yagE, yagF, yagG, yagH, xynR, argF, argL, ykgS, insB3, insA3, yagJ, [yagK] |
| RA | 557,635 | A→T | L36Q (CTG→CAG) | folD ← | bifunctional methylenetetrahydrofolate dehydrogenase/methenyltetrahydrofolate cyclohydrolase |
| MC JC | 678,556 | Δ9,295 bp | IS5‑mediated | [djlB]–gltI | [djlB], ybeT, ybeU, djlC, hscC, rihA, gltL, gltK, gltJ, sroC, gltI |
| RA | 997,952 | G→A | D29N (GAT→AAT) | elfA → | putative laminin‑binding fimbrial subunit |
| JC JC | 1,105,376 | IS2 (–) +5 bp | intergenic (+83/‑34) | csgC → / → ymdA | curlin chaperone/uncharacterized protein YmdA |
| RA | 1,196,220 | C→T | H366H (CAC→CAT) | icd → | isocitrate dehydrogenase |
| RA | 1,196,232 | C→T | T370T (ACC→ACT) | icd → | isocitrate dehydrogenase |
| RA | 1,196,245 | T→C | L375M (TTA→CTG) | icd → | isocitrate dehydrogenase |
| RA | 1,196,247 | A→G | L375M (TTA→CTG) | icd → | isocitrate dehydrogenase |
| RA | 1,196,277 | C→T | N385N (AAC→AAT) | icd → | isocitrate dehydrogenase |
| RA | 1,196,280 | G→C | A386A (GCG→GCC) | icd → | isocitrate dehydrogenase |
| RA | 1,196,283 | A→G | K387K (AAA→AAG) | icd → | isocitrate dehydrogenase |
| RA | 1,196,292 | C→T | T390T (ACC→ACT) | icd → | isocitrate dehydrogenase |
| RA | 1,196,304 | G→A | E394E (GAG→GAA) | icd → | isocitrate dehydrogenase |
| JC JC | 1,293,268 | IS5 (–) +4 bp | intergenic (‑346/‑256) | hns ← / → tdk | DNA‑binding transcriptional dual regulator H‑NS/thymidine/deoxyuridine kinase |
| RA | 1,301,998 | A→G | S273G (AGC→GGC) | oppA → | oligopeptide ABC transporter periplasmic binding protein |
| RA | 1,337,394 | A→G | S522G (AGC→GGC) | acnA → | aconitate hydratase 1 |
| RA | 1,507,867 | G→A | E363K (GAG→AAG) | rlhA → | 23S rRNA 5‑hydroxycytidine C2501 synthase |
| RA | 1,652,331 | T→C | intergenic (+2346/+397) | ydfD → / ← ynfP | lysis protein/protein YnfP |
| RA | 1,991,340 | G→A | P94S (CCG→TCG) | yecA ← | putative iron‑binding protein YecA |
| RA | 2,032,423 | G→A | V219V (GTC→GTT) | yedJ ← | putative HD superfamily phosphohydrolase YedJ |
| RA | 2,173,363 | Δ2 bp | intergenic (‑490/+918) | gatD ← / ← gatB | galactitol‑1‑phosphate 5‑dehydrogenase/galactitol‑specific PTS enzyme IIB component |
| RA | 2,200,082 | G→C | intergenic (+2784/‑197) | yehF → / → yehI | PF05406 family protein YehF/DUF4132 domain‑containing protein YehI |
| JC JC | 2,317,491 | IS2 (–) +5 bp | coding (2382‑2386/2850 nt) | rcsC ← | histidine kinase RcsC |
| JC JC | 2,406,780 | IS1 (–) +8 bp | intergenic (‑139/‑774) | lrhA ← / → alaA | DNA‑binding transcriptional dual regulator LrhA/glutamate‑‑pyruvate aminotransferase AlaA |
| RA | 2,630,697 | T→G | V124V (GTT→GTG) | yfgI → | nalidixic acid resistance protein YfgI |
| RA | 2,867,455 | G→A | Q33* (CAG→TAG) | rpoS ← | RNA polymerase sigma factor RpoS |
| RA | 2,964,554 | C→T | W201* (TGG→TAG) | thyA ← | thymidylate synthase |
| MC JC | 3,369,587 | Δ21 bp | coding (744‑764/876 nt) | nanK ← | N‑acetylmannosamine kinase |
| JC JC | 3,433,571 | IS2 (–) +5 bp | intergenic (‑11/‑115) | smf ← / → def | protein Smf/peptide deformylase |
| RA | 3,439,441 | G→A | N23N (AAC→AAT) | yhdN ← | DUF1992 domain‑containing protein YhdN |
| RA | 3,446,306 | G→A | R80R (CGC→CGT) | rpsH ← | 30S ribosomal subunit protein S8 |
| RA | 3,486,205 | C→A | T29K (ACG→AAG) | crp → | DNA‑binding transcriptional dual regulator CRP |
| RA | 3,505,521 | G→A | A167V (GCG→GTG) | yhfS ← | putative aminotransferase YhfS |
| JC JC | 3,533,238 | IS2 (+) +5 bp | coding (421‑425/1623 nt) | pck → | phosphoenolpyruvate carboxykinase (ATP) |
| RA | 3,560,455 | +G | intergenic (+589/+167) | rtcR → / ← glpG | DNA‑binding transcriptional activator RtcR/rhomboid protease GlpG |
| RA | 3,585,798 | G→A | G342G (GGC→GGT) | ggt ← | glutathione hydrolase proenzyme |
| RA | 3,602,616 | G→A | L44L (CTC→CTT) | ftsE ← | cell division protein FtsE |
| RA | 3,636,603 | G→A | Q270* (CAG→TAG) | yhiN ← | putative oxidoreductase YhiN |
| RA | 3,647,488 | G→A | G397E (GGA→GAA) | gor → | glutathione reductase (NADPH) |
| RA | 3,669,496 | G→T | intergenic (‑308/‑96) | ccp ← / → treF | cytochrome c peroxidase/cytoplasmic trehalase |
| MC JC | 3,829,684 | Δ4 bp | coding (740‑743/1392 nt) | xanP → | xanthine:H(+) symporter XanP |
| RA | 3,851,491 | C→T | A432T (GCG→ACG) | ilvB ← | acetohydroxy acid synthase I subunit IlvB |
| RA | 3,854,736 | C→T | T272M (ACG→ATG) | emrD → | multidrug efflux pump EmrD |
| RA | 3,856,859 | G→A | V149I (GTT→ATT) | yidI → | putative inner membrane protein YidI |
| RA | 3,915,109 | G→A | A31V (GCC→GTC) | glmU ← | fused N‑acetylglucosamine‑1‑phosphate uridyltransferase and glucosamine‑1‑phosphate acetyltransferase |
| RA | 3,927,286 | G→A | T44T (ACG→ACA) | asnA → | asparagine synthetase A |
| RA | 3,947,818 | G→A | R50R (CGC→CGT) | hdfR ← | DNA‑binding transcriptional dual regulator HdfR |
| RA | 3,949,882 | G→A | P30S (CCC→TCC) | yifB ← | putative magnesium chelatase YifB |
| RA | 3,951,109 | G→A | intergenic (+552/‑1092) | ilvX → / → ilvM | uncharacterized protein IlvX/acetolactate synthase II subunit IlvM |
| RA | 3,958,114 | G→A | G49S (GGT→AGT) | ilvC → | ketol‑acid reductoisomerase (NADP(+)) |
| RA | 3,961,606 | G→A | A310A (GCG→GCA) | rep → | ATP‑dependent DNA helicase Rep |
| RA | 3,963,982 | G→A | A83V (GCT→GTT) | gpp ← | guanosine‑5'‑triphosphate,3'‑diphosphate phosphatase |
| RA | 3,966,882 | G→A | D156N (GAT→AAT) | rho → | transcription termination factor Rho |
| RA | 3,969,673 | G→A | V215M (GTG→ATG) | wzzE → | enterobacterial common antigen polysaccharide co‑polymerase |
| RA | 3,987,423 | G→A | P154S (CCG→TCG) | hemY ← | protein HemY |
| RA | 3,995,228 | G→A | G156E (GGA→GAA) | dapF → | diaminopimelate epimerase |
| RA | 3,997,332 | G→A | Q50Q (CAG→CAA) | yigB → | 5‑amino‑6‑(5‑phospho‑D‑ribitylamino)uracil phosphatase |
| RA | 4,022,269 | G→A | V18I (GTC→ATC) | tatB → | twin arginine protein translocation system ‑ TatB protein |
| RA | 4,025,758 | G→A | K257K (AAG→AAA) | ubiD → | 3‑octaprenyl‑4‑hydroxybenzoate decarboxylase |
| RA | 4,034,915 | G→A | S103N (AGC→AAC) | hemG → | protoporphyrinogen oxidase |
| RA | 4,039,508 | G→A | noncoding (1990/2905 nt) | rrlA → | 23S ribosomal RNA |
| RA | 4,041,484 | G→A | S172S (AGC→AGT) | mobA ← | molybdenum cofactor guanylyltransferase |
| RA | 4,047,990 | G→A | W342* (TGG→TAG) | polA → | DNA polymerase I |
| RA | 4,053,510 | C→T | intergenic (+92/+137) | hemN → / ← yshB | coproporphyrinogen III dehydrogenase/uncharacterized protein YshB |
| RA | 4,060,209 | C→T | N601N (AAC→AAT) | bipA → | 50S ribosomal subunit assembly factor BipA |
| MC JC | 4,077,654 | Δ87 bp | coding (206‑292/990 nt) | fabY → | putative fatty acid biosynthesis enzyme FabY |
| RA | 4,116,856 | C→T | D123N (GAT→AAT) | glpK ← | glycerol kinase |
| RA | 4,124,865 | G→A | A649V (GCG→GTG) | priA ← | primosomal protein N' |
| RA | 4,296,381 | +GC | intergenic (+587/+55) | gltP → / ← yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| RA | 4,490,854 | T→G | T96P (ACC→CCC) | idnR ← | DNA‑binding transcriptional dual regulator IdnR |
| RA | 4,617,537 | C→G | T72R (ACG→AGG) | deoC → | deoxyribose‑phosphate aldolase |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 1196316 | 1211420 | 15105 | 17 [15] | [15] 17 | [icd]–mcrA | [icd],C0293,ymfD,ymfE,lit,intE,xisE,ymfH,ymfI,ymfJ,ymfK,ymfT,ymfL,ymfM,ymfN,ymfR,beeE,ymfQ,ycfK,tfaP,tfaE,pinE,mcrA |
| * | * | ÷ | NC_000913 | 1978495 | 1979270–1978504 | 10–776 | 92 [0] | [0] 118 | insB5–insA5 | insB5,insA5 |
| * | * | ÷ | NC_000913 | 3423919–3424234 | 3424389–3424238 | 5–471 | 17 [14] | [16] 17 | rrlD | 23S ribosomal RNA |
| * | * | ÷ | NC_000913 | 3888429 | 3891106 | 2678 | 183 [1] | [0] 156 | tnaC–[tnaB] | tnaC,tnaA,[tnaB] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 90 (0.900) | 57/590 | 0.4 | 100% | intergenic (+253/‑69) | ychE/insH21 | MarC family putative inner membrane protein YchE/IS5 family transposase and trans‑activator |
| ? | NC_000913 | 1300698 = | 0 (0.000) | intergenic (+151/‑484) | insH21/oppA | IS5 family transposase and trans‑activator/oligopeptide ABC transporter periplasmic binding protein | |||||
| * | ? | NC_000913 | = 1397238 | NA (NA) | 92 (0.910) | 69/598 | 0.2 | 100% | noncoding (1195/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 1978494 | 0 (0.000) | intergenic (‑297/+24) | flhD/insB5 | DNA‑binding transcriptional dual regulator FlhD/IS1 family protein InsB | |||||
| * | ? | NC_000913 | 1979271 = | 0 (0.000) | 117 (1.160) | 76/598 | 0.1 | 100% | intergenic (‑56/‑482) | insA5/uspC | IS1 family protein InsA/universal stress protein C |
| ? | NC_000913 | = 2102947 | NA (NA) | pseudogene (443/446 nt) | wbbL | interrupted rhamnosyltransferase WbbL | |||||
| * | ? | NC_000913 | 2068941 = | NA (NA) | 54 (0.530) | 42/598 | 0.9 | 67.5% | noncoding (1331/1331 nt) | IS2 | repeat region |
| ? | NC_000913 | = 2456896 | 26 (0.260) | intergenic (‑84/+119) | sixA/fadJ | phosphohistidine phosphatase SixA/3‑hydroxyacyl‑CoA dehydrogenase FadJ | |||||
| * | ? | NC_000913 | = 2140129 | 25 (0.250) | 44 (0.440) | 36/590 | 1.1 | 63.9% | coding (1484/1854 nt) | asmA | putative assembly protein AsmA |
| ? | NC_000913 | 2140138 = | 25 (0.250) | coding (1475/1854 nt) | asmA | putative assembly protein AsmA | |||||
| * | ? | NC_000913 | 2288919 = | NA (NA) | 182 (1.800) | 116/598 | 0.0 | 99.5% | noncoding (1195/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 3888428 | 1 (0.010) | intergenic (+236/‑7) | mnmE/tnaC | 5‑carboxymethylaminomethyluridine‑tRNA synthase GTPase subunit/tnaAB operon leader peptide | |||||
| * | ? | NC_000913 | 2288919 = | NA (NA) | 114 (1.130) | 76/596 | 0.1 | 65.9% | noncoding (1195/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 4506068 | 59 (0.590) | coding (782/1119 nt) | nanY | 2,7‑anhydro‑N‑acetylneuraminate hydratase | |||||
| * | ? | NC_000913 | = 2290113 | NA (NA) | 117 (1.160) | 69/596 | 0.2 | 67.2% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | 4506065 = | 57 (0.570) | coding (779/1119 nt) | nanY | 2,7‑anhydro‑N‑acetylneuraminate hydratase | |||||
| * | ? | NC_000913 | 2456892 = | 26 (0.260) | 50 (0.490) | 41/598 | 0.9 | 65.8% | intergenic (‑80/+123) | sixA/fadJ | phosphohistidine phosphatase SixA/3‑hydroxyacyl‑CoA dehydrogenase FadJ |
| ? | NC_000913 | = 2997691 | NA (NA) | noncoding (1/1331 nt) | IS2 | repeat region | |||||
| * | ? | NC_000913 | 2996361 = | NA (NA) | 40 (0.400) | 32/598 | 1.4 | 23.3% | noncoding (1331/1331 nt) | IS2 | repeat region |
| ? | NC_000913 | 3366918 = | 132 (1.310) | pseudogene (164/175 nt) | yhcE | putative uncharacterized protein YhcE | |||||
| * | ? | NC_000913 | 3094602 = | 80 (0.790) | 67 (0.660) | 56/598 | 0.4 | 43.0% | coding (479/981 nt) | yggR | Type II/IV secretion system family protein |
| ? | NC_000913 | = 3094791 | 98 (0.970) | coding (290/981 nt) | yggR | Type II/IV secretion system family protein | |||||
| * | ? | NC_000913 | 3186096 = | NA (NA) | 34 (0.340) | 29/598 | 1.6 | 20.7% | noncoding (1/1331 nt) | IS2 | repeat region |
| ? | NC_000913 | = 3366922 | 130 (1.290) | pseudogene (168/175 nt) | yhcE | putative uncharacterized protein YhcE | |||||
| * | ? | NC_000913 | = 3653230 | NA (NA) | 157 (1.550) | 90/598 | 0.1 | 100% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | 3891107 = | 0 (0.000) | coding (872/1248 nt) | tnaB | tryptophan:H(+) symporter TnaB | |||||
| * | ? | NC_000913 | = 4217985 | 25 (0.250) | 97 (0.960) | 71/596 | 0.2 | 79.5% | coding (877/1305 nt) | aceA | isocitrate lyase |
| ? | NC_000913 | 4217992 = | 25 (0.250) | coding (884/1305 nt) | aceA | isocitrate lyase | |||||
| * | ? | NC_000913 | 4405599 = | 28 (0.280) | 78 (0.800) | 57/580 | 0.4 | 74.2% | coding (913/1299 nt) | purA | adenylosuccinate synthetase |
| ? | NC_000913 | = 4405595 | 27 (0.280) | coding (909/1299 nt) | purA | adenylosuccinate synthetase | |||||
| * | ? | NC_000913 | 4542682 = | 137 (1.360) | 41 (0.420) | 30/580 | 1.5 | 23.8% | intergenic (+49/‑433) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | 4542996 = | 129 (1.320) | intergenic (+363/‑119) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | = 4542690 | 144 (1.420) | 34 (0.350) | 30/580 | 1.5 | 20.2% | intergenic (+57/‑425) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | = 4542986 | 129 (1.320) | intergenic (+353/‑129) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||