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 | 126,351 | Δ1 bp | 24.6% | coding (657/1893 nt) | aceF → | pyruvate dehydrogenase, dihydrolipoyltransacetylase component E2 |
| RA | 126,352 | Δ1 bp | 23.2% | coding (658/1893 nt) | aceF → | pyruvate dehydrogenase, dihydrolipoyltransacetylase component E2 |
| RA | 126,353 | Δ1 bp | 26.1% | coding (659/1893 nt) | aceF → | pyruvate dehydrogenase, dihydrolipoyltransacetylase component E2 |
| RA | 126,354 | Δ1 bp | 26.1% | coding (660/1893 nt) | aceF → | pyruvate dehydrogenase, dihydrolipoyltransacetylase component E2 |
| RA | 126,355 | Δ1 bp | 26.1% | coding (661/1893 nt) | aceF → | pyruvate dehydrogenase, dihydrolipoyltransacetylase component E2 |
| RA | 126,356 | Δ1 bp | 26.1% | coding (662/1893 nt) | aceF → | pyruvate dehydrogenase, dihydrolipoyltransacetylase component E2 |
| RA | 126,357 | Δ1 bp | 23.9% | coding (663/1893 nt) | aceF → | pyruvate dehydrogenase, dihydrolipoyltransacetylase component E2 |
| RA | 126,358 | Δ1 bp | 31.0% | coding (664/1893 nt) | aceF → | pyruvate dehydrogenase, dihydrolipoyltransacetylase component E2 |
| JC | 126,359 | Δ9 bp | 27.2% | coding (665‑673/1893 nt) | aceF → | pyruvate dehydrogenase, dihydrolipoyltransacetylase component E2 |
| RA | 158,169 | C→A | 25.3% | A320S (GCC→TCC) | pcnB ← | poly(A) polymerase |
| RA | 199,522 | T→A | 5.3% | V532E (GTA→GAA) | bamA → | BamABCDE complex OM biogenesis outer membrane pore‑forming assembly factor |
| MC JC | 257,908 | Δ776 bp | 100% | [crl] | [crl] | |
| RA | 1,096,644 | A→T | 7.1% | M268L (ATG→TTG) | ycdU → | putative inner membrane protein |
| RA | 1,466,276 | T→C | 9.9% | pseudogene (885/2513 nt) | ydbA → | pseudogene, autotransporter homolog; interrupted by IS2 and IS30 |
| RA | 1,466,280 | A→C | 7.4% | pseudogene (889/2513 nt) | ydbA → | pseudogene, autotransporter homolog; interrupted by IS2 and IS30 |
| RA | 1,524,324 | C→T | 7.8% | Q340* (CAG→TAG) | yncE → | ATP‑binding protein, periplasmic, function unknown |
| RA | 1,529,218 | C→T | 14.3% | pseudogene (1317/2037 nt) | rhsE → | pseudogene, Rhs family |
| RA | 1,708,724 | G→A | 11.0% | K602K (AAG→AAA) | rsxC → | SoxR iron‑sulfur cluster reduction factor component; putative membrane‑associated NADH oxidoreductase of electron transport complex |
| RA | 1,708,726 | T→G | 14.6% | L603R (CTG→CGG) | rsxC → | SoxR iron‑sulfur cluster reduction factor component; putative membrane‑associated NADH oxidoreductase of electron transport complex |
| RA | 1,708,766 | C→T | 10.3% | V616V (GTC→GTT) | rsxC → | SoxR iron‑sulfur cluster reduction factor component; putative membrane‑associated NADH oxidoreductase of electron transport complex |
| RA | 1,708,805 | T→C | 13.2% | R629R (CGT→CGC) | rsxC → | SoxR iron‑sulfur cluster reduction factor component; putative membrane‑associated NADH oxidoreductase of electron transport complex |
| RA | 1,756,280 | C→A | 5.3% | R195S (CGT→AGT) | pykF → | pyruvate kinase I |
| RA | 1,756,664 | G→T | 73.3% | E323* (GAA→TAA) | pykF → | pyruvate kinase I |
| JC JC | 1,757,115 | IS1 (+) +9 bp | 8.5% | intergenic (+5/‑298) | pykF → / → lpp | pyruvate kinase I/murein lipoprotein |
| JC | 1,915,110 | Δ204 bp | 83.5% | coding (222‑425/699 nt) | proQ ← | RNA chaperone, putative ProP translation regulator |
| RA | 2,173,360 | Δ1 bp | 8.8% | pseudogene (3/442 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 | 2,173,361 | 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 | 2,580,432 | Δ1 bp | 5.5% | coding (797/2004 nt) | tktB → | transketolase 2, thiamine triphosphate‑binding |
| RA | 2,867,239 | Δ1 bp | 100% | coding (313/993 nt) | rpoS ← | RNA polymerase, sigma S (sigma 38) factor |
| RA | 2,919,550 | Δ1 bp | 5.5% | coding (1197/1341 nt) | gudX ← | glucarate dehydratase‑related protein, substrate unknown |
| JC JC | 3,049,604 | IS5 (+) +4 bp | 100% | coding (1061‑1064/1095 nt) | gcvT ← | aminomethyltransferase, tetrahydrofolate‑dependent, subunit (T protein) of glycine cleavage complex |
| RA | 3,505,962 | G→A | 7.8% | A20V (GCG→GTG) | yhfS ← | FNR‑regulated pyridoxal phosphate‑dependent aminotransferase family 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 |
| RA | 3,586,710 | Δ1 bp | 9.3% | coding (114/1743 nt) | ggt ← | gamma‑glutamyltranspeptidase |
| RA | 3,815,809 | Δ1 bp | 79.3% | intergenic (‑41/+25) | pyrE ← / ← rph | orotate phosphoribosyltransferase/ribonuclease PH (defective);enzyme; Degradation of RNA; RNase PH |
| RA | 4,187,507 | A→C | 7.2% | N720H (AAC→CAC) | rpoC → | RNA polymerase, beta prime subunit |
| RA | 4,296,190 | A→G | 17.8% | intergenic (+396/+246) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,268 | T→C | 32.3% | intergenic (+474/+168) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,286 | C→T | 19.7% | intergenic (+492/+150) | 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 |
| RA | 4,350,122 | A→T | 6.6% | L514H (CTC→CAC) | dcuS ← | sensory histidine kinase in two‑component regulatory system with DcuR, regulator of anaerobic fumarate respiration |
| RA | 4,444,152 | T→C | 8.0% | V14A (GTT→GCT) | tamB → | translocation and assembly module for autotransporter export, inner membrane subunit |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 1978503–1979267 | 1979289 | 23–787 | 28 [0] | [25] 31 | insB1–insA | insB1, insA |
| * | * | ÷ | NC_000913 | 3798812 | 3799563 | 752 | 28 [26] | [26] 28 | [waaU]–[waaZ] | [waaU], [waaZ] |
| Unassigned new junction evidence... | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 1207790 = | 30 (0.390) | 18 (0.250) | 18/510 | NT | 43.3% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | 1209619 = | 19 (0.270) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 29 (0.380) | 25 (0.350) | 21/510 | NT | 51.9% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | = 1209602 | 19 (0.270) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 36 (0.480) | 32/534 | 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 | = 1651548 | NA (NA) | 11 (0.140) | 11/542 | NT | 13.6% | noncoding (706/706 nt) | IS2 | repeat region |
| ? | NC_000913 | 1755716 = | 70 (0.920) | coding (19/1413 nt) | pykF | pyruvate kinase I | |||||
| * | ? | NC_000913 | 1879829 = | 74 (0.980) | 3 (0.040) | 3/538 | NT | 3.9% | coding (120/360 nt) | yeaR | DUF1971 family protein, nitrate‑inducible |
| ? | NC_000913 | 2514274 = | NA (NA) | noncoding (2/1345 nt) | IS186 | repeat region | |||||
| * | ? | NC_000913 | = 1978502 | 0 (0.000) | 22 (0.300) | 21/526 | NT | 100% | intergenic (‑305/+16) | flhD/insB1 | flagellar class II regulon transcriptional activator, with FlhC/IS1 transposase B |
| ? | NC_000913 | 1979279 = | 0 (0.000) | intergenic (‑64/‑474) | insA/uspC | IS1 repressor TnpA/universal stress protein | |||||