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 | 260,173 | Δ13,782 bp | IS5‑mediated | proB–[ykfC] | 19 genes proB, proA, thrW, ykfI, yafW, ykfH, ykfG, yafX, ykfF, ykfB, yafY, yafZ, ykfA, perR, insN, insI1, insN, eyeA, [ykfC] |
| RA | 284,535 | T→G | A445A (GCT→GCG) | yagF → | D‑xylonate dehydratase |
| RA | 579,127 | T→C | intergenic (‑234/+57) | borD ← / ← ybcV | prophage lipoprotein BorD/DUF1398 domain‑containing protein YbcV |
| RA | 579,134 | T→C | intergenic (‑241/+50) | borD ← / ← ybcV | prophage lipoprotein BorD/DUF1398 domain‑containing protein YbcV |
| RA | 635,355 | G→A | R8* (CGA→TGA) N405N (AAC→AAT) |
ybdM ← ybdN ← |
ParB‑like nuclease domain‑containing protein YbdM putative PAPS reductase/DUF3440 domain‑containing protein YbdN |
| RA | 696,582 | C→T | noncoding (35/75 nt) | glnV ← | tRNA‑Gln |
| RA | 811,531 | G→A | G384D (GGT→GAT) V4I (GTT→ATT) |
bioF → bioC → |
8‑amino‑7‑oxononanoate synthase malonyl‑acyl carrier protein methyltransferase |
| RA | 1,097,494 | T→A | intergenic (+665/+71) | ycdU → / ← serX | uncharacterized protein YcdU/tRNA‑Ser |
| RA | 1,169,836 | A→G | L180P (CTG→CCG) | ldtC ← | L,D‑transpeptidase LdtC |
| RA | 1,189,980 | A→G | T156T (ACT→ACC) | phoP ← | DNA‑binding transcriptional dual regulator PhoP |
| MC JC | 1,299,499 | Δ1,199 bp | insH21 | insH21 | |
| RA | 1,301,992 | A→T | N271Y (AAT→TAT) | oppA → | oligopeptide ABC transporter periplasmic binding protein |
| RA | 1,306,736 | T→G | S325A (TCC→GCC) | oppF → | murein tripeptide ABC transporter/oligopeptide ABC transporter ATP binding subunit OppF |
| RA | 1,337,394 | A→G | S522G (AGC→GGC) | acnA → | aconitate hydratase 1 |
| RA | 1,358,859 | T→C | Y110C (TAT→TGT) | puuP ← | putrescine:H(+) symporter PuuP |
| RA | 1,643,679 | A→T | L209Q (CTG→CAG) | ydfU ← | protein YdfU |
| RA | 1,652,331 | T→C | intergenic (+2346/+397) | ydfD → / ← ynfP | lysis protein/protein YnfP |
| RA | 1,705,108 | G→A | G54R (GGG→AGG) | cnu → | H‑NS‑ and StpA‑binding protein |
| MC JC | 1,978,503 | Δ776 bp | insB5–insA5 | insB5, insA5 | |
| RA | 2,040,433 | C→A | A319D (GCC→GAC) | msrP → | protein‑L‑methionine sulfoxide reductase catalytic subunit MsrP |
| JC JC | 2,050,482 | IS150 (–) +3 bp | coding (5545‑5547/7077 nt) | yeeJ → | inverse autotransporter adhesin |
| RA | 2,173,363 | Δ2 bp | intergenic (‑490/+918) | gatD ← / ← gatB | galactitol‑1‑phosphate 5‑dehydrogenase/galactitol‑specific PTS enzyme IIB component |
| JC JC | 2,176,322 | IS1 (–) +9 bp | intergenic (‑1/+20) | gatZ ← / ← gatY | putative tagatose‑1,6‑bisphosphate aldolase 2 chaperone/tagatose‑1,6‑bisphosphate aldolase 2 |
| RA | 2,867,455 | G→A | Q33* (CAG→TAG) | rpoS ← | RNA polymerase sigma factor RpoS |
| RA | 3,388,041 | T→G | T50P (ACG→CCG) | aaeB ← | aromatic carboxylic acid efflux pump subunit AaeB |
| RA | 3,560,455 | +G | intergenic (+589/+167) | rtcR → / ← glpG | DNA‑binding transcriptional activator RtcR/rhomboid protease GlpG |
| RA | 3,707,947 | C→A | intergenic (‑242/+669) | dppA ← / ← proK | dipeptide ABC transporter periplasmic binding protein/tRNA‑Pro |
| RA | 3,938,645 | T→A | V140E (GTG→GAG) | rbsR → | DNA‑binding transcriptional dual regulator RbsR |
| RA | 4,132,697 | G→A | E28K (GAG→AAG) | metF → | 5,10‑methylenetetrahydrofolate reductase |
| RA | 4,223,638 | T→C | intergenic (‑10/‑190) | iclR ← / → metH | DNA‑binding transcriptional repressor IclR/cobalamin‑dependent methionine synthase |
| RA | 4,296,381 | +GC | intergenic (+587/+55) | gltP → / ← yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| RA | 4,510,238 | T→G | intergenic (+445/+452) | insO → / ← fecE | IS911B regulator fragment/ferric citrate ABC transporter ATP binding subunit |
| RA | 4,566,642 | G→A | S202L (TCG→TTG) | yjiN ← | DUF445 domain‑containing protein YjiN |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 3423816–3424231 | 3424482–3424239 | 9–667 | 39 [37] | [38] 40 | [rrlD] | [rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 275149 | NA (NA) | 41 (0.380) | 35/598 | 2.2 | 28.3% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | 697928 = | 104 (0.960) | coding (1250/1665 nt) | asnB | asparagine synthetase B | |||||
| * | ? | NC_000913 | 317762 = | 92 (0.850) | 41 (0.380) | 35/598 | 2.2 | 30.8% | coding (558/594 nt) | rclC | DUF417 domain‑containing inner membrane protein RclC |
| ? | NC_000913 | = 1470516 | NA (NA) | noncoding (1221/1221 nt) | IS30 | repeat region | |||||
| * | ? | NC_000913 | = 317763 | 88 (0.820) | 42 (0.390) | 30/594 | 2.8 | 32.3% | coding (557/594 nt) | rclC | DUF417 domain‑containing inner membrane protein RclC |
| ? | NC_000913 | 1469296 = | NA (NA) | noncoding (1/1221 nt) | IS30 | repeat region | |||||
| * | ? | NC_000913 | 474976 = | 62 (0.570) | 42 (0.390) | 30/596 | 2.8 | 40.4% | coding (186/861 nt) | tesB | acyl‑CoA thioesterase II |
| ? | NC_000913 | = 1470516 | NA (NA) | noncoding (1221/1221 nt) | IS30 | repeat region | |||||
| * | ? | NC_000913 | = 474977 | 63 (0.590) | 38 (0.350) | 32/592 | 2.5 | 37.6% | coding (185/861 nt) | tesB | acyl‑CoA thioesterase II |
| ? | NC_000913 | 1469296 = | NA (NA) | noncoding (1/1221 nt) | IS30 | repeat region | |||||
| * | ? | NC_000913 | = 566774 | 97 (0.890) | 79 (0.730) | 30/594 | 2.8 | 43.5% | pseudogene (91/93 nt) | renD | protein RenD |
| ? | NC_000913 | 568036 = | 109 (1.010) | pseudogene (2/213 nt) | renD | protein RenD | |||||
| * | ? | NC_000913 | 566777 = | NA (NA) | 34 (0.310) | 30/596 | 2.8 | 27.5% | noncoding (1/1258 nt) | IS3 | repeat region |
| ? | NC_000913 | = 572471 | 90 (0.830) | coding (6/456 nt) | ybcN | DNA base‑flipping protein | |||||
| * | ? | NC_000913 | 678436 = | 53 (0.490) | 43 (0.400) | 30/594 | 2.8 | 44.8% | coding (1022/1428 nt) | djlB | J domain‑containing protein DjlB |
| ? | NC_000913 | 1469296 = | NA (NA) | noncoding (1/1221 nt) | IS30 | repeat region | |||||
| * | ? | NC_000913 | = 678437 | 51 (0.470) | 57 (0.530) | 39/598 | 1.8 | 52.8% | coding (1023/1428 nt) | djlB | J domain‑containing protein DjlB |
| ? | NC_000913 | = 1470516 | NA (NA) | noncoding (1221/1221 nt) | IS30 | repeat region | |||||
| * | ? | NC_000913 | = 679348 | 94 (0.870) | 44 (0.410) | 37/598 | 2.0 | 31.9% | coding (59/555 nt) | ybeT | Sel1 repeat‑containing protein YbeT |
| ? | NC_000913 | 687851 = | NA (NA) | noncoding (1195/1195 nt) | IS5 | repeat region | |||||
| * | ? | NC_000913 | = 891857 | 88 (0.810) | 35 (0.320) | 32/598 | 2.6 | 28.5% | coding (674/723 nt) | nfsA | NADPH‑dependent nitro/quinone reductase NfsA |
| ? | NC_000913 | 1469295 = | NA (NA) | pseudogene (50/50 nt) | ydbA | putative outer membrane protein, N‑terminal fragment | |||||
| * | ? | NC_000913 | 1207790 = | 45 (0.420) | 85 (0.830) | 62/566 | 0.4 | 62.4% | coding (290/630 nt) | ycfK | protein StfP |
| ? | NC_000913 | 1209619 = | 60 (0.580) | intergenic (‑500/‑66) | tfaE/pinE | putative tail fiber assembly protein TfaE/site‑specific DNA recombinase | |||||
| * | ? | NC_000913 | = 1207805 | 49 (0.450) | 61 (0.590) | 44/566 | 1.2 | 53.4% | coding (305/630 nt) | ycfK | protein StfP |
| ? | NC_000913 | = 1209602 | 60 (0.580) | intergenic (‑483/‑83) | tfaE/pinE | putative tail fiber assembly protein TfaE/site‑specific DNA recombinase | |||||
| * | ? | NC_000913 | = 1293199 | 67 (0.620) | 88 (0.810) | 54/598 | 0.8 | 56.8% | intergenic (‑277/‑328) | hns/tdk | DNA‑binding transcriptional dual regulator H‑NS/thymidine/deoxyuridine kinase |
| ? | NC_000913 | 2101749 = | NA (NA) | noncoding (1195/1195 nt) | IS5 | repeat region | |||||
| * | ? | NC_000913 | 1299499 = | NA (NA) | 86 (0.790) | 64/598 | 0.4 | 86.0% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | 1300735 = | 14 (0.130) | intergenic (+188/‑447) | insH21/oppA | IS5 family transposase and trans‑activator/oligopeptide ABC transporter periplasmic binding protein | |||||
| * | ? | NC_000913 | 1396044 = | NA (NA) | 44 (0.410) | 38/598 | 1.9 | 29.5% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | 1470408 = | 105 (0.970) | noncoding (1113/1221 nt) | IS30 | repeat region | |||||
| * | ? | NC_000913 | 1469296 = | NA (NA) | 53 (0.490) | 40/594 | 1.7 | 37.9% | noncoding (1/1221 nt) | IS30 | repeat region |
| ? | NC_000913 | = 1995730 | 87 (0.810) | coding (76/177 nt) | yecU | protein YecU | |||||
| * | ? | NC_000913 | 1469296 = | NA (NA) | 51 (0.470) | 40/598 | 1.7 | 38.1% | noncoding (1/1221 nt) | IS30 | repeat region |
| ? | NC_000913 | 2980510 = | 83 (0.770) | coding (126/693 nt) | ygeA | amino acid racemase YgeA | |||||
| * | ? | NC_000913 | 1469296 = | NA (NA) | 44 (0.410) | 32/598 | 2.6 | 40.4% | noncoding (1/1221 nt) | IS30 | repeat region |
| ? | NC_000913 | = 2999636 | 65 (0.600) | coding (256/756 nt) | actS | amidase activator | |||||
| * | ? | NC_000913 | = 1470411 | 112 (1.030) | 31 (0.290) | 29/598 | 3.0 | 21.7% | noncoding (1116/1221 nt) | IS30 | repeat region |
| ? | NC_000913 | 2101749 = | NA (NA) | noncoding (1195/1195 nt) | IS5 | repeat region | |||||
| * | ? | NC_000913 | = 1470516 | NA (NA) | 55 (0.510) | 41/598 | 1.6 | 38.7% | noncoding (1221/1221 nt) | IS30 | repeat region |
| ? | NC_000913 | 1995729 = | 87 (0.800) | coding (75/177 nt) | yecU | protein YecU | |||||
| * | ? | NC_000913 | = 1470516 | NA (NA) | 61 (0.570) | 44/594 | 1.4 | 41.8% | noncoding (1221/1221 nt) | IS30 | repeat region |
| ? | NC_000913 | 2698402 = | 85 (0.790) | coding (149/636 nt) | pgpC | phosphatidylglycerophosphatase C | |||||
| * | ? | NC_000913 | = 1470516 | NA (NA) | 65 (0.600) | 45/596 | 1.3 | 43.3% | noncoding (1221/1221 nt) | IS30 | repeat region |
| ? | NC_000913 | = 2980511 | 85 (0.790) | coding (125/693 nt) | ygeA | amino acid racemase YgeA | |||||
| * | ? | NC_000913 | 1907353 = | 87 (0.810) | 51 (0.470) | 36/594 | 2.1 | 37.0% | coding (83/210 nt) | cspC | transcription antiterminator and regulator of mRNA stability CspC |
| ? | NC_000913 | 2068941 = | NA (NA) | noncoding (1331/1331 nt) | IS2 | repeat region | |||||
| * | ? | NC_000913 | 2001042 = | 37 (0.340) | 88 (0.810) | 67/598 | 0.3 | 70.4% | intergenic (‑18/+28) | fliZ/fliA | DNA‑binding transcriptional regulator FliZ/RNA polymerase sigma factor FliA |
| ? | NC_000913 | 2101749 = | NA (NA) | noncoding (1195/1195 nt) | IS5 | repeat region | |||||
| * | ? | NC_000913 | = 2001045 | 36 (0.330) | 65 (0.600) | 54/596 | 0.8 | 64.4% | intergenic (‑21/+25) | fliZ/fliA | DNA‑binding transcriptional regulator FliZ/RNA polymerase sigma factor FliA |
| ? | NC_000913 | = 2290113 | NA (NA) | noncoding (1/1195 nt) | IS5 | repeat region | |||||
| * | ? | NC_000913 | 2288919 = | NA (NA) | 56 (0.520) | 43/598 | 1.5 | 32.8% | noncoding (1195/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 3804461 | 115 (1.060) | coding (656/936 nt) | waaS | lipopolysaccharide core biosynthesis protein WaaS | |||||
| * | ? | NC_000913 | = 2290113 | NA (NA) | 61 (0.560) | 48/598 | 1.1 | 62.2% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 2406443 | 37 (0.340) | coding (199/939 nt) | lrhA | DNA‑binding transcriptional dual regulator LrhA | |||||
| * | ? | NC_000913 | = 2290113 | NA (NA) | 47 (0.430) | 35/598 | 2.2 | 28.7% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | 3804458 = | 117 (1.080) | coding (659/936 nt) | waaS | lipopolysaccharide core biosynthesis protein WaaS | |||||
| * | ? | NC_000913 | = 2290113 | NA (NA) | 32 (0.300) | 30/598 | 2.9 | 26.7% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 3890225 | 88 (0.810) | intergenic (+80/‑11) | tnaA/tnaB | tryptophanase/tryptophan:H(+) symporter TnaB | |||||
| * | ? | NC_000913 | 2406440 = | 38 (0.350) | 58 (0.530) | 42/598 | 1.6 | 60.4% | coding (202/939 nt) | lrhA | DNA‑binding transcriptional dual regulator LrhA |
| ? | NC_000913 | = 3131340 | NA (NA) | noncoding (1195/1195 nt) | IS5 | repeat region | |||||
| * | ? | NC_000913 | = 2698403 | 85 (0.780) | 45 (0.420) | 35/598 | 2.2 | 34.6% | coding (148/636 nt) | pgpC | phosphatidylglycerophosphatase C |
| ? | NC_000913 | = 4508679 | NA (NA) | noncoding (1/1221 nt) | IS30 | repeat region | |||||
| * | ? | NC_000913 | 2999635 = | 66 (0.610) | 59 (0.540) | 43/598 | 1.5 | 47.2% | coding (257/756 nt) | actS | amidase activator |
| ? | NC_000913 | 4507459 = | NA (NA) | noncoding (1221/1221 nt) | IS30 | repeat region | |||||
| * | ? | NC_000913 | 3186096 = | NA (NA) | 34 (0.310) | 29/598 | 3.0 | 31.8% | noncoding (1/1331 nt) | IS2 | repeat region |
| ? | NC_000913 | = 3261929 | 73 (0.670) | coding (490/2295 nt) | tdcE | 2‑ketobutyrate formate‑lyase/pyruvate formate‑lyase 4 | |||||
| * | ? | NC_000913 | 3186096 = | NA (NA) | 60 (0.560) | 45/596 | 1.3 | 57.7% | noncoding (1/1331 nt) | IS2 | repeat region |
| ? | NC_000913 | = 3487231 | 44 (0.410) | coding (441/2103 nt) | yhfK | putative transporter YhfK | |||||
| * | ? | NC_000913 | = 3187426 | NA (NA) | 43 (0.400) | 39/596 | 1.8 | 36.1% | noncoding (1331/1331 nt) | IS2 | repeat region |
| ? | NC_000913 | 3261925 = | 76 (0.700) | coding (494/2295 nt) | tdcE | 2‑ketobutyrate formate‑lyase/pyruvate formate‑lyase 4 | |||||
| * | ? | NC_000913 | = 3187426 | NA (NA) | 88 (0.820) | 62/594 | 0.5 | 69.3% | noncoding (1331/1331 nt) | IS2 | repeat region |
| ? | NC_000913 | 3487227 = | 39 (0.360) | coding (437/2103 nt) | yhfK | putative transporter YhfK | |||||
| * | ? | NC_000913 | 3365556 = | NA (NA) | 50 (0.470) | 39/590 | 1.8 | 36.5% | noncoding (1195/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | 3890222 = | 88 (0.810) | intergenic (+77/‑14) | tnaA/tnaB | tryptophanase/tryptophan:H(+) symporter TnaB | |||||
| * | ? | NC_000913 | = 3534370 | 62 (0.570) | 38 (0.350) | 29/598 | 3.0 | 38.0% | coding (1553/1623 nt) | pck | phosphoenolpyruvate carboxykinase (ATP) |
| ? | NC_000913 | 4507459 = | NA (NA) | noncoding (1221/1221 nt) | IS30 | repeat region | |||||
| * | ? | NC_000913 | 3583428 = | NA (NA) | 39 (0.360) | 35/598 | 2.2 | 41.9% | noncoding (1/768 nt) | IS1 | repeat region |
| ? | NC_000913 | = 4123916 | 54 (0.500) | coding (541/1026 nt) | cytR | DNA‑binding transcriptional repressor CytR | |||||
| * | ? | NC_000913 | 3652036 = | NA (NA) | 86 (0.790) | 66/598 | 0.4 | 57.3% | noncoding (1195/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | 3888626 = | 64 (0.590) | intergenic (+117/‑104) | tnaC/tnaA | tnaAB operon leader peptide/tryptophanase | |||||
| * | ? | NC_000913 | = 3653230 | NA (NA) | 84 (0.770) | 56/598 | 0.7 | 56.8% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 3888629 | 64 (0.590) | intergenic (+120/‑101) | tnaC/tnaA | tnaAB operon leader peptide/tryptophanase | |||||