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 |
| JC JC | 528,897 | IS5 (+) +4 bp | 35.0% | pseudogene (258‑261/491 nt) | ybbD → | pseudogene |
| 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 | 2,173,361 | 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 |
| JC | 2,347,240 | Δ88 bp | 3.0% | intergenic (+90/‑57) | nrdA → / → nrdB | ribonucleoside‑diphosphate reductase 1, alpha subunit/ribonucleoside‑diphosphate reductase 1, beta subunit, ferritin‑like protein |
| JC | 2,521,360 | Δ156 bp | 3.6% | intergenic (+32/+78) | lysV → / ← xapR | tRNA‑Lys/transcriptional activator of xapAB |
| JC | 2,798,351 | Δ3 bp | 2.8% | coding (143‑145/405 nt) | stpA ← | DNA binding protein, nucleoid‑associated |
| RA | 2,836,077 | A→G | 6.0% | V450A (GTG→GCG) | hypF ← | carbamoyl phosphate phosphatase and [NiFe] hydrogenase maturation protein |
| 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 |
| JC | 3,815,859 | Δ82 bp | 83.5% | [rph]–[rph] | [rph], [rph] | |
| RA | 4,116,407 | C→A | 100% | M272I (ATG→ATT) | glpK ← | glycerol kinase |
| RA | 4,183,258 | G→A | 100% | E672K (GAA→AAA) | rpoB → | RNA polymerase, beta subunit |
| RA | 4,296,190 | A→G | 9.5% | intergenic (+396/+246) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,191 | A→C | 14.4% | intergenic (+397/+245) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,268 | T→C | 32.8% | intergenic (+474/+168) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,286 | C→T | 23.8% | intergenic (+492/+150) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,303 | A→G | 9.0% | intergenic (+509/+133) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,304 | A→C | 10.1% | 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 | 1299490 | 1300710 | 1221 | 49 [48] | [44] 51 | ychE/oppA | UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein |
| * | * | ÷ | NC_000913 | 3423905–3424234 | 3424462–3424238 | 5–558 | 55 [48] | [48] 49 | rrlD | 23S ribosomal RNA of rrnD operon |
| Unassigned new junction evidence... | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 49871 | 114 (0.940) | 4 (0.030) | 4/476 | NT | 3.5% | coding (49/480 nt) | folA | dihydrofolate reductase |
| ? | NC_000913 | = 49877 | 112 (0.950) | coding (55/480 nt) | folA | dihydrofolate reductase | |||||
| * | ? | NC_000913 | = 257907 | 0 (0.000) | 127 (1.080) | 82/476 | 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 | = 907278 | 107 (0.880) | 6 (0.050) | 6/478 | NT | 5.5% | coding (1005/1431 nt) | ybjT | putative NAD‑dependent oxidoreductase |
| ? | NC_000913 | = 907329 | 103 (0.870) | coding (954/1431 nt) | ybjT | putative NAD‑dependent oxidoreductase | |||||
| * | ? | NC_000913 | = 915489 | 78 (0.640) | 3 (0.030) | 3/476 | NT | 3.7% | coding (559/696 nt) | aqpZ | aquaporin Z |
| ? | NC_000913 | = 915572 | 81 (0.690) | coding (476/696 nt) | aqpZ | aquaporin Z | |||||
| * | ? | NC_000913 | 1207790 = | 58 (0.480) | 52 (0.460) | 40/460 | NT | 50.7% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | 1209619 = | 47 (0.410) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 56 (0.460) | 53 (0.470) | 44/460 | NT | 51.6% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | = 1209602 | 47 (0.410) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1242594 | 96 (0.790) | 3 (0.030) | 3/456 | NT | 3.3% | coding (487/915 nt) | ldcA | murein tetrapeptide carboxypeptidase; LD‑carboxypeptidase A |
| ? | NC_000913 | = 1242576 | 88 (0.780) | coding (505/915 nt) | ldcA | murein tetrapeptide carboxypeptidase; LD‑carboxypeptidase A | |||||
| * | ? | NC_000913 | = 1293199 | 175 (1.440) | 5 (0.040) | 5/492 | NT | 2.8% | 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) | 42 (0.350) | 36/484 | 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 | = 1392324 | 133 (1.090) | 6 (0.050) | 5/492 | NT | 4.3% | coding (334/900 nt) | pgrR | murein peptide degradation regulator |
| ? | NC_000913 | 1396044 = | NA (NA) | noncoding (1/1195 nt) | IS5 | repeat region | |||||
| * | ? | NC_000913 | 2319571 = | 103 (0.850) | 3 (0.030) | 3/472 | NT | 2.8% | coding (306/2850 nt) | rcsC | hybrid sensory kinase in two‑component regulatory system with RcsB and YojN |
| ? | NC_000913 | 2319597 = | 107 (0.920) | coding (280/2850 nt) | rcsC | hybrid sensory kinase in two‑component regulatory system with RcsB and YojN | |||||
| * | ? | NC_000913 | 2514273 = | NA (NA) | 7 (0.060) | 7/484 | NT | NA | noncoding (1/1345 nt) | IS186 | repeat region |
| ? | NC_000913 | 4295812 = | NA (NA) | intergenic (+18/+624) | gltP/yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein | |||||
| * | ? | NC_000913 | = 2515615 | NA (NA) | 3 (0.020) | 3/488 | NT | 2.2% | noncoding (1343/1345 nt) | IS186 | repeat region |
| ? | NC_000913 | = 4295817 | 131 (1.090) | intergenic (+23/+619) | gltP/yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein | |||||
| * | ? | NC_000913 | 2852106 = | 127 (1.040) | 3 (0.030) | 3/476 | NT | 2.4% | coding (243/273 nt) | hypC | hydrogenase maturation protein |
| ? | NC_000913 | 2852166 = | 125 (1.060) | coding (31/1122 nt) | hypD | hydrogenase maturation protein | |||||
| * | ? | NC_000913 | = 3558994 | 33 (0.270) | 89 (0.760) | 64/472 | NT | 72.8% | coding (727/1599 nt) | rtcR | sigma 54‑dependent transcriptional regulator of rtcBA expression |
| ? | NC_000913 | 3560035 = | 35 (0.300) | pseudogene (419/606 nt) | glpR | pseudogene, DNA‑binding transcriptional repressor;regulator; Energy metabolism, carbon: Anaerobic respiration; repressor of the glp operon | |||||
| * | ? | NC_000913 | 3581359 = | 180 (1.480) | 3 (0.030) | 3/478 | NT | 1.6% | coding (222/489 nt) | yhhY | aminoacyl nucleotide detoxifying acetyltransferase |
| ? | NC_000913 | 3581422 = | 193 (1.630) | coding (285/489 nt) | yhhY | aminoacyl nucleotide detoxifying acetyltransferase | |||||
| * | ? | NC_000913 | = 4240750 | 116 (0.950) | 4 (0.030) | 4/472 | NT | 3.4% | intergenic (+15/+29) | psiE/xylE | phosphate starvation inducible protein/D‑xylose transporter |
| ? | NC_000913 | = 4240758 | 114 (0.980) | intergenic (+23/+21) | psiE/xylE | phosphate starvation inducible protein/D‑xylose transporter | |||||