mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.26.0
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Predicted mutations | ||||||
|---|---|---|---|---|---|---|
| evidence | position | mutation | freq | annotation | gene | description |
| RA | 444,755 | G→T | 54.6% | E25* (GAA→TAA) | yajQ → | phage Phi6 host factor, ATP/GTP binding protein |
| JC JC | 572,356 | IS2 (–) +5 bp | 69.1% | intergenic (+105/‑8) | ybcM → / → ylcH | DLP12 prophage; putative DNA‑binding transcriptional regulator/uncharacterized protein, DLP12 prophage |
| RA | 630,242 | A→G | 7.8% | M117V (ATG→GTG) | cstA → | carbon starvation protein involved in peptide utilization; APC peptide transporter family protein |
| RA | 696,739 | C→A | 5.2% | noncoding (2/77 nt) | metU ← | tRNA‑Met |
| RA | 1,529,218 | C→T | 100% | pseudogene (1317/2037 nt) | rhsE → | pseudogene, Rhs family |
| MC JC | 1,978,503 | Δ776 bp | 100% | insB1–insA | insB1, insA | |
| RA | 2,113,377 | G→C | 6.9% | intergenic (‑316/+57) | rfbB ← / ← wcaN | dTDP‑glucose 4,6 dehydratase, NAD(P)‑binding/putative regulatory subunit for GalU |
| 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 | 2,304,798 | T→C | 7.0% | intergenic (+405/+310) | eco → / ← mqo | ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain |
| RA | 2,966,765 | G→A | 11.4% | P557L (CCG→CTG) | ptsP ← | PEP‑protein phosphotransferase enzyme I; GAF domain containing protein |
| RA | 3,560,071 | Δ1 bp | 5.2% | pseudogene (383/606 nt) | glpR ← | pseudogene, DNA‑binding transcriptional repressor;regulator; Energy metabolism, carbon: Anaerobic respiration; repressor of the glp operon |
| RA | 3,560,072 | Δ1 bp | 5.2% | pseudogene (382/606 nt) | glpR ← | pseudogene, DNA‑binding transcriptional repressor;regulator; Energy metabolism, carbon: Anaerobic respiration; repressor of the glp operon |
| RA | 3,560,113 | A→C | 6.9% | pseudogene (341/606 nt) | glpR ← | pseudogene, DNA‑binding transcriptional repressor;regulator; Energy metabolism, carbon: Anaerobic respiration; repressor of the glp operon |
| RA | 3,560,329 | G→T | 60.5% | pseudogene (125/606 nt) | glpR ← | pseudogene, DNA‑binding transcriptional repressor;regulator; Energy metabolism, carbon: Anaerobic respiration; repressor of the glp operon |
| RA | 3,560,455 | +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 | 3,560,460 | A→T | 9.5% | pseudogene (146/150 nt) | glpR ← | pseudogene, DNA‑binding transcriptional repressor;regulator; Energy metabolism, carbon: Anaerobic respiration; repressor of the glp operon |
| RA | 3,815,809 | +A | 10.2% | intergenic (‑41/+25) | pyrE ← / ← rph | orotate phosphoribosyltransferase/ribonuclease PH (defective);enzyme; Degradation of RNA; RNase PH |
| RA | 3,884,067 | T→A | 17.6% | intergenic (‑338/‑269) | dnaA ← / → rpmH | chromosomal replication initiator protein DnaA, DNA‑binding transcriptional dual regulator/50S ribosomal subunit protein L34 |
| RA | 3,950,469 | T→G | 22.8% | intergenic (+49/‑38) | ilvL → / → ilvX | ilvG operon leader peptide/uncharacterized protein |
| RA | 3,992,954 | C→T | 13.4% | S601L (TCG→TTG) | cyaA → | adenylate cyclase |
| RA | 4,116,706 | T→G | 100% | K173Q (AAA→CAA) | glpK ← | glycerol kinase |
| RA | 4,187,507 | A→C | 100% | N720H (AAC→CAC) | rpoC → | RNA polymerase, beta prime subunit |
| RA | 4,296,060 | C→T | 6.1% | intergenic (+266/+376) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,190 | A→G | 17.4% | intergenic (+396/+246) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,191 | A→C | 19.2% | intergenic (+397/+245) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,268 | T→C | 29.1% | intergenic (+474/+168) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,286 | C→T | 21.7% | intergenic (+492/+150) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,303 | A→G | 12.8% | intergenic (+509/+133) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,304 | A→C | 12.7% | intergenic (+510/+132) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,380 | +CG | 100% | intergenic (+586/+56) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 3423816–3424490 | 3424490 | 1–675 | 66 [64] | [64] 65 | [rrlD] | [rrlD] |
| Unassigned new junction evidence... | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 200412 | 130 (0.950) | 3 (0.020) | 3/514 | NT | 2.1% | intergenic (+52/‑70) | bamA/skp | BamABCDE complex OM biogenesis outer membrane pore‑forming assembly factor/periplasmic chaperone |
| ? | NC_000913 | = 200419 | 159 (1.200) | intergenic (+59/‑63) | bamA/skp | BamABCDE complex OM biogenesis outer membrane pore‑forming assembly factor/periplasmic chaperone | |||||
| * | ? | NC_000913 | = 257907 | 0 (0.000) | 111 (0.840) | 70/512 | NT | 100% | intergenic (+8/‑769) | crl/crl | pseudogene, sigma factor‑binding protein, RNA polymerase holoenzyme formation stimulator;regulator; Surface structures; transcriptional regulator of cryptic csgA gene for curli surface fibers/pseudogene, sigma factor‑binding protein, RNA polymerase holoenzyme formation stimulator;regulator; Surface structures; transcriptional regulator of cryptic csgA gene for curli surface fibers |
| ? | NC_000913 | 258684 = | 0 (0.000) | pseudogene (9/331 nt) | crl | pseudogene, sigma factor‑binding protein, RNA polymerase holoenzyme formation stimulator;regulator; Surface structures; transcriptional regulator of cryptic csgA gene for curli surface fibers | |||||
| * | ? | NC_000913 | 273955 = | NA (NA) | 5 (0.040) | 4/528 | NT | 6.8% | noncoding (1195/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 572051 | 69 (0.510) | coding (598/798 nt) | ybcM | DLP12 prophage; putative DNA‑binding transcriptional regulator | |||||
| * | ? | NC_000913 | 1207790 = | 61 (0.450) | 60 (0.470) | 45/496 | NT | 51.0% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | 1209619 = | 58 (0.450) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 60 (0.440) | 41 (0.320) | 31/496 | NT | 41.8% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | = 1209602 | 58 (0.450) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1242594 | 138 (1.010) | 3 (0.020) | 3/492 | NT | 2.3% | coding (487/915 nt) | ldcA | murein tetrapeptide carboxypeptidase; LD‑carboxypeptidase A |
| ? | NC_000913 | = 1242576 | 125 (0.980) | coding (505/915 nt) | ldcA | murein tetrapeptide carboxypeptidase; LD‑carboxypeptidase A | |||||
| * | ? | NC_000913 | = 1293199 | 226 (1.660) | 3 (0.020) | 3/528 | NT | 1.3% | intergenic (‑277/‑328) | hns/tdk | global DNA‑binding transcriptional dual regulator H‑NS/thymidine kinase/deoxyuridine kinase |
| ? | NC_000913 | 1299499 = | NA (NA) | noncoding (1/1195 nt) | IS5 | repeat region | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 54 (0.400) | 41/520 | 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 | = 1482221 | 112 (0.820) | 4 (0.030) | 4/506 | NT | 3.6% | intergenic (+20/+34) | ynbD/azoR | putative phosphatase inner membrane protein/NADH‑azoreductase, FMN‑dependent |
| ? | NC_000913 | = 1482229 | 108 (0.830) | intergenic (+28/+26) | ynbD/azoR | putative phosphatase inner membrane protein/NADH‑azoreductase, FMN‑dependent | |||||
| * | ? | NC_000913 | = 2988001 | 297 (2.180) | 3 (0.020) | 3/526 | NT | 1.0% | coding (466/633 nt) | yqeH | putative LuxR family transcriptional regulator |
| ? | NC_000913 | = 2988008 | 292 (2.150) | coding (473/633 nt) | yqeH | putative LuxR family transcriptional regulator | |||||