mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.33.1 revision 8505477f25b3
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Predicted mutations | ||||||
|---|---|---|---|---|---|---|
| evidence | position | mutation | freq | annotation | gene | description |
| RA | 70,412 | T→G | 5.8% | L9R (CTG→CGG) | araC → | ara regulon transcriptional activator; autorepressor |
| RA | 70,852 | C→A | 87.3% | L156I (CTT→ATT) | araC → | ara regulon transcriptional activator; autorepressor |
| RA | 208,106 | T→A | 5.4% | I994N (ATC→AAC) | dnaE → | DNA polymerase III alpha subunit |
| MC JC | 257,908 | Δ776 bp | 100% | [crl] | [crl] | |
| RA | 509,007 | G→A | 5.5% | V791V (GTC→GTT) | copA ← | copper transporter |
| RA | 612,648 | G→T | 5.7% | intergenic (‑154/‑89) | fepA ← / → fes | ferrienterobactin outer membrane transporter/enterobactin/ferrienterobactin esterase |
| RA | 626,675 | C→T | 5.2% | R202R (CGC→CGT) | entE → | 2,3‑dihydroxybenzoate‑AMP ligase component of enterobactin synthase multienzyme complex |
| RA | 639,654 | T→C | 5.6% | intergenic (+146/‑99) | ahpC → / → ahpF | alkyl hydroperoxide reductase, C22 subunit/alkyl hydroperoxide reductase, F52a subunit, FAD/NAD(P)‑binding |
| RA | 639,657 | G→A | 5.5% | intergenic (+149/‑96) | ahpC → / → ahpF | alkyl hydroperoxide reductase, C22 subunit/alkyl hydroperoxide reductase, F52a subunit, FAD/NAD(P)‑binding |
| RA | 1,048,429 | C→T | 5.5% | W88* (TGG→TAG) ‡ | gfcC ← | putative O‑antigen capsule production periplasmic protein |
| RA | 1,048,430 | A→G | 5.4% | W88R (TGG→CGG) ‡ | gfcC ← | putative O‑antigen capsule production periplasmic protein |
| RA | 1,097,158 | C→T | 9.5% | intergenic (+329/+407) | ycdU → / ← serX | putative inner membrane protein/tRNA‑Ser |
| RA | 1,113,548 | T→C | 5.5% | intergenic (+142/‑31) | opgH → / → yceK | OPG biosynthetic ACP‑dependent transmembrane UDP‑glucose beta‑1,2 glycosyltransferase; nutrient‑dependent cell size regulator, FtsZ assembly antagonist/outer membrane integrity lipoprotein |
| RA | 1,529,218 | C→T | 100% | pseudogene (1317/2037 nt) | rhsE → | pseudogene, Rhs family |
| RA | 1,689,817 | C→A | 5.0% | intergenic (+66/‑35) | manA → / → ydgA | mannose‑6‑phosphate isomerase/DUF945 family protein |
| RA | 1,698,585 | T→G | 5.8% | E199A (GAA→GCA) | malI ← | transcriptional repressor of Mal regulon |
| RA | 1,698,587 | T→A | 5.1% | A198A (GCA→GCT) ‡ | malI ← | transcriptional repressor of Mal regulon |
| RA | 1,698,589 | C→A | 5.0% | A198S (GCA→TCA) ‡ | malI ← | transcriptional repressor of Mal regulon |
| RA | 1,703,251 | A→T | 5.4% | intergenic (+17/+17) | add → / ← ydgJ | adenosine deaminase/putative oxidoreductase |
| RA | 1,703,252 | A→T | 5.4% | intergenic (+18/+16) | add → / ← ydgJ | adenosine deaminase/putative oxidoreductase |
| RA | 1,840,795 | G→A | 5.4% | L203L (CTC→CTT) | ynjF ← | CDP‑alcohol phosphatidyltransferase family inner membrane protein |
| RA | 1,840,798 | C→T | 5.6% | S202S (TCG→TCA) ‡ | ynjF ← | CDP‑alcohol phosphatidyltransferase family inner membrane protein |
| RA | 1,840,799 | G→C | 5.4% | S202W (TCG→TGG) ‡ | ynjF ← | CDP‑alcohol phosphatidyltransferase family inner membrane protein |
| RA | 1,840,800 | A→G | 6.2% | S202P (TCG→CCG) ‡ | ynjF ← | CDP‑alcohol phosphatidyltransferase family inner membrane protein |
| RA | 1,840,803 | T→C | 5.4% | K201E (AAG→GAG) | ynjF ← | CDP‑alcohol phosphatidyltransferase family inner membrane protein |
| RA | 1,863,800 | T→C | 5.7% | intergenic (+34/‑50) | gapA → / → yeaD | glyceraldehyde‑3‑phosphate dehydrogenase A/D‑hexose‑6‑phosphate epimerase‑like protein |
| RA | 1,863,801 | T→G | 6.5% | intergenic (+35/‑49) | gapA → / → yeaD | glyceraldehyde‑3‑phosphate dehydrogenase A/D‑hexose‑6‑phosphate epimerase‑like protein |
| RA | 1,863,802 | C→A | 5.9% | intergenic (+36/‑48) | gapA → / → yeaD | glyceraldehyde‑3‑phosphate dehydrogenase A/D‑hexose‑6‑phosphate epimerase‑like protein |
| RA | 1,863,803 | G→A | 5.9% | intergenic (+37/‑47) | gapA → / → yeaD | glyceraldehyde‑3‑phosphate dehydrogenase A/D‑hexose‑6‑phosphate epimerase‑like protein |
| RA | 1,892,358 | C→T | 6.9% | G293D (GGT→GAT) | yoaA ← | putative ATP‑dependent helicase, DinG family |
| RA | 1,892,363 | A→G | 7.7% | Y291Y (TAT→TAC) | yoaA ← | putative ATP‑dependent helicase, DinG family |
| RA | 1,965,088 | C→T | 5.6% | V368V (GTG→GTA) | flhB ← | flagellin export apparatus, substrate specificity protein |
| MC JC | 1,978,503 | Δ776 bp | 100% | insB1–insA | insB1, insA | |
| RA | 1,999,231 | T→A | 6.0% | T84S (ACT→TCT) | dcyD ← | D‑cysteine desulfhydrase, PLP‑dependent |
| RA | 2,025,578 | G→A | 7.1% | S23N (AGT→AAT) ‡ | yedP → | putative mannosyl‑3‑phosphoglycerate phosphatase |
| RA | 2,025,579 | T→C | 7.0% | S23S (AGT→AGC) ‡ | yedP → | putative mannosyl‑3‑phosphoglycerate phosphatase |
| RA | 2,081,353 | C→G | 5.0% | intergenic (‑91/+28) | sbmC ← / ← dacD | DNA gyrase inhibitor/D‑alanyl‑D‑alanine carboxypeptidase; penicillin‑binding protein 6b |
| RA | 2,173,361 | Δ2 bp | 100% | pseudogene (1‑2/442 nt) | gatC ← | pseudogene, galactitol‑specific enzyme IIC component of PTS;transport; Transport of small molecules: Carbohydrates, organic acids, alcohols; PTS system galactitol‑specific enzyme IIC |
| RA | 2,939,592 | C→A | 100% | S75R (AGC→AGA) | fucR → | l‑fucose operon activator |
| RA | 2,940,099 | A→C | 100% | *244C (TGA→TGC) | fucR → | l‑fucose operon activator |
| RA | 3,049,511 | Δ1 bp | 73.5% | coding (39/390 nt) | gcvH ← | glycine cleavage complex lipoylprotein |
| RA | 3,183,345:1 | +T | 5.9% | intergenic (+22/+468) | zupT → / ← ribB | zinc transporter/3,4‑dihydroxy‑2‑butanone‑4‑phosphate synthase |
| RA | 3,183,350 | Δ1 bp | 5.8% | intergenic (+27/+463) | zupT → / ← ribB | zinc transporter/3,4‑dihydroxy‑2‑butanone‑4‑phosphate synthase |
| RA | 3,233,708 | A→G | 5.9% | intergenic (+25/+20) | fadH → / ← higA | 2,4‑dienoyl‑CoA reductase, NADH and FMN‑linked/antitoxinof the HigB‑HigA toxin‑antitoxin system |
| RA | 3,233,709 | A→T | 6.1% | intergenic (+26/+19) | fadH → / ← higA | 2,4‑dienoyl‑CoA reductase, NADH and FMN‑linked/antitoxinof the HigB‑HigA toxin‑antitoxin system |
| RA | 3,233,710 | C→T | 6.2% | intergenic (+27/+18) | fadH → / ← higA | 2,4‑dienoyl‑CoA reductase, NADH and FMN‑linked/antitoxinof the HigB‑HigA toxin‑antitoxin system |
| RA | 3,324,952 | A→G | 7.0% | intergenic (‑41/+49) | folP ← / ← ftsH | 7,8‑dihydropteroate synthase/protease, ATP‑dependent zinc‑metallo |
| RA | 3,324,955 | A→G | 7.5% | intergenic (‑44/+46) | folP ← / ← ftsH | 7,8‑dihydropteroate synthase/protease, ATP‑dependent zinc‑metallo |
| RA | 3,324,956 | C→T | 7.6% | intergenic (‑45/+45) | folP ← / ← ftsH | 7,8‑dihydropteroate synthase/protease, ATP‑dependent zinc‑metallo |
| RA | 3,324,959 | C→T | 7.0% | intergenic (‑48/+42) | folP ← / ← ftsH | 7,8‑dihydropteroate synthase/protease, ATP‑dependent zinc‑metallo |
| RA | 3,560,455:1 | +G | 100% | 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 | 3,771,187 | G→C | 7.7% | P65A (CCT→GCT) | yibH ← | putative membrane fusion protein (MFP) component of efflux pump |
| RA | 3,771,192 | G→C | 7.2% | A63G (GCG→GGG) | yibH ← | putative membrane fusion protein (MFP) component of efflux pump |
| RA | 3,967,560 | A→T | 100% | I382F (ATC→TTC) | rho → | transcription termination factor |
| RA | 4,065,787 | C→T | 5.2% | intergenic (‑21/+22) | yihO ← / ← yihP | putative sulphoquinovose importer/putative 2,3‑dihydroxypropane‑1‑sulphonate exporter, membrane protein |
| RA | 4,065,790 | A→G | 5.2% | intergenic (‑24/+19) | yihO ← / ← yihP | putative sulphoquinovose importer/putative 2,3‑dihydroxypropane‑1‑sulphonate exporter, membrane protein |
| RA | 4,296,190 | A→G | 22.2% | intergenic (+396/+246) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,191 | A→C | 27.3% | intergenic (+397/+245) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,268 | T→C | 27.0% | intergenic (+474/+168) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,286 | C→T | 15.9% | intergenic (+492/+150) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,303 | A→G | 10.8% | intergenic (+509/+133) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,304 | A→C | 10.9% | intergenic (+510/+132) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,380:1 | +CG | 100% | intergenic (+586/+56) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,400,322 | T→C | 5.7% | L12P (CTG→CCG) | hfq → | global sRNA chaperone; HF‑I, host factor for RNA phage Q beta replication |
| RA | 4,637,693 | T→A | 5.4% | L333* (TTA→TAA) | creC → | sensory histidine kinase in two‑component regulatory system with CreB or PhoB |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 3423817–3424234 | 3424499–3424238 | 5–683 | 53 [52] | [52] 53 | [rrlD] | [rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 274347 = | NA (NA) | 5 (0.050) | 5/550 | NT | NA | noncoding (803/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | 274410 = | NA (NA) | noncoding (740/1195 nt) | IS5 | repeat region | |||||
| * | ? | NC_000913 | = 315651 | NA (NA) | 3 (0.030) | 3/548 | NT | NA | noncoding (423/1255 nt) | IS3 | repeat region |
| ? | NC_000913 | = 315703 | NA (NA) | noncoding (475/1255 nt) | IS3 | repeat region | |||||
| * | ? | NC_000913 | 1154501 = | 93 (0.870) | 5 (0.050) | 5/564 | NT | 5.1% | coding (390/1023 nt) | yceG | septation protein, ampicillin sensitivity |
| ? | NC_000913 | 1467910 = | NA (NA) | noncoding (1331/1331 nt) | IS2 | repeat region | |||||
| * | ? | NC_000913 | 1207790 = | 65 (0.610) | 55 (0.550) | 48/532 | NT | 51.1% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | 1209619 = | 44 (0.440) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 64 (0.600) | 42 (0.420) | 40/532 | NT | 44.6% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | = 1209602 | 44 (0.440) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 136 (1.290) | 121/556 | NT | 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 | |||||
| * | ? | NC_000913 | 1411899 = | 111 (1.040) | 6 (0.060) | 6/512 | NT | 6.0% | coding (50/936 nt) | ttcA | tRNA s(2)C32 thioltransferase, iron sulfur cluster protein |
| ? | NC_000913 | = 1434958 | 87 (0.900) | pseudogene (51/51 nt) | ttcC | pseudogene, prophage Rac integration site ttcA duplication;Phage or Prophage Related | |||||
| * | ? | NC_000913 | 4324601 = | 76 (0.710) | 4 (0.040) | 4/548 | NT | 5.0% | coding (565/789 nt) | phnC | phosphonate ABC transporter ATPase |
| ? | NC_000913 | 4324671 = | 77 (0.740) | coding (495/789 nt) | phnC | phosphonate ABC transporter ATPase | |||||
| * | ? | NC_000913 | = 4542690 | 126 (1.180) | 13 (0.130) | 13/546 | NT | 8.8% | intergenic (+57/‑425) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) |
| ? | NC_000913 | = 4542986 | 146 (1.410) | intergenic (+353/‑129) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) | |||||