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 |
| MC JC | 257,908 | Δ776 bp | 100% | [crl] | [crl] | |
| JC | 521,734 | Δ90 bp | 4.8% | coding (1319‑1408/2415 nt) | ybbP → | putative ABC transporter permease |
| RA | 1,097,158 | C→T | 6.5% | intergenic (+329/+407) | ycdU → / ← serX | putative inner membrane protein/tRNA‑Ser |
| JC JC | 1,293,124 | IS5 (+) +4 bp | 12.4% | intergenic (‑202/‑400) | hns ← / → tdk | global DNA‑binding transcriptional dual regulator H‑NS/thymidine kinase/deoxyuridine kinase |
| MC JC | 1,299,499 | Δ1,199 bp | 100% | intergenic (+254/‑485) | ychE → / → oppA | UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein |
| RA | 1,356,662 | C→T | 6.8% | S150N (AGC→AAC) | sapA ← | antimicrobial peptide transport ABC transporter periplasmic binding protein |
| RA | 1,466,579 | G→C | 6.5% | pseudogene (1188/2513 nt) | ydbA → | pseudogene, autotransporter homolog; interrupted by IS2 and IS30 |
| RA | 1,529,218 | C→T | 100% | pseudogene (1317/2037 nt) | rhsE → | pseudogene, Rhs family |
| RA | 1,708,844 | C→G | 10.1% | A642A (GCC→GCG) | rsxC → | SoxR iron‑sulfur cluster reduction factor component; putative membrane‑associated NADH oxidoreductase of electron transport complex |
| RA | 1,708,847 | G→A | 8.6% | E643E (GAG→GAA) | rsxC → | SoxR iron‑sulfur cluster reduction factor component; putative membrane‑associated NADH oxidoreductase of electron transport complex |
| RA | 1,708,854 | C→G | 7.8% | Q646E (CAA→GAA) | rsxC → | SoxR iron‑sulfur cluster reduction factor component; putative membrane‑associated NADH oxidoreductase of electron transport complex |
| RA | 1,708,985 | G→C | 6.9% | A689A (GCG→GCC) | rsxC → | SoxR iron‑sulfur cluster reduction factor component; putative membrane‑associated NADH oxidoreductase of electron transport complex |
| RA | 1,778,806 | T→A | 10.8% | K166* (AAA→TAA) | ydiP ← | putative DNA‑binding transcriptional regulator |
| RA | 2,173,359 | Δ1 bp | 6.1% | pseudogene (4/442 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 | 2,304,523 | G→C | 7.6% | intergenic (+130/+585) | eco → / ← mqo | ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain |
| RA | 2,455,411 | A→G | 5.4% | L79P (CTG→CCG) | yfcV ← | putative fimbrial‑like adhesin protein |
| RA | 3,277,038 | Δ1 bp | 6.1% | coding (37/336 nt) | prlF → | antitoxin of the SohA(PrlF)‑YhaV toxin‑antitoxin system |
| 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 | 10.7% | 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 | Δ1 bp | 55.0% | intergenic (‑41/+25) | pyrE ← / ← rph | orotate phosphoribosyltransferase/ribonuclease PH (defective);enzyme; Degradation of RNA; RNase PH |
| JC | 3,815,859 | Δ82 bp | 3.5% | [rph]–[rph] | [rph], [rph] | |
| JC | 3,815,909 | Δ10 bp | 5.2% | pseudogene (632‑641/669 nt) | rph ← | ribonuclease PH (defective);enzyme; Degradation of RNA; RNase PH |
| RA | 4,116,407 | C→A | 100% | M272I (ATG→ATT) | glpK ← | glycerol kinase |
| RA | 4,117,005 | T→A | 7.4% | D73V (GAT→GTT) | glpK ← | glycerol kinase |
| RA | 4,183,258 | G→A | 100% | E672K (GAA→AAA) | rpoB → | RNA polymerase, beta subunit |
| RA | 4,296,155 | T→C | 10.4% | intergenic (+361/+281) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,190 | A→G | 28.7% | intergenic (+396/+246) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,191 | A→C | 34.1% | intergenic (+397/+245) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,268 | T→C | 23.0% | intergenic (+474/+168) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,286 | C→T | 13.7% | intergenic (+492/+150) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,303 | A→G | 8.7% | intergenic (+509/+133) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,304 | A→C | 6.9% | 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 | 582991 | 584639 | 1649 | 45 [41] | [42] 43 | [tfaX]–appY | [tfaX], appY |
| * | * | ÷ | NC_000913 | 1211041 | 1212738 | 1698 | 43 [42] | [38] 44 | [mcrA]–[ycgX] | [mcrA], icdC, iraM, [ycgX] |
| * | * | ÷ | NC_000913 | 1978503–1979269 | 1979692 | 424–1190 | 44 [0] | [42] 44 | insB1–insA | insB1, insA |
| Unassigned new junction evidence... | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 1096961 = | 59 (0.550) | 15 (0.200) | 7/380 | NT | 22.5% | intergenic (+132/+604) | ycdU/serX | putative inner membrane protein/tRNA‑Ser |
| ? | NC_000913 | = 1097503 | 62 (0.820) | intergenic (+674/+62) | ycdU/serX | putative inner membrane protein/tRNA‑Ser | |||||
| * | ? | NC_000913 | 1207790 = | 42 (0.390) | 46 (0.450) | 36/508 | NT | 54.9% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | 1209619 = | 36 (0.350) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 43 (0.400) | 65 (0.640) | 59/508 | NT | 63.0% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | = 1209602 | 36 (0.350) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | 1746589 = | 95 (0.880) | 5 (0.050) | 5/524 | NT | 5.2% | noncoding (74/77 nt) | valW | tRNA‑Val |
| ? | NC_000913 | 1746610 = | 91 (0.870) | intergenic (+18/‑90) | valW/ydhR | tRNA‑Val/putative monooxygenase | |||||
| * | ? | NC_000913 | = 1896969 | 86 (0.810) | 4 (0.040) | 3/532 | NT | 4.4% | coding (38/1365 nt) | sdaA | L‑serine dehydratase 1 |
| ? | NC_000913 | 2514273 = | NA (NA) | noncoding (1/1345 nt) | IS186 | repeat region | |||||
| * | ? | NC_000913 | = 1978502 | 0 (0.000) | 38 (0.360) | 32/524 | 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 | |||||
| * | ? | NC_000913 | 2736907 = | 116 (1.070) | 4 (0.040) | 4/534 | NT | 3.4% | intergenic (+24/‑247) | bamD/raiA | BamABCDE complex OM biogenesis lipoprotein/cold shock protein associated with 30S ribosomal subunit |
| ? | NC_000913 | 4502090 = | NA (NA) | noncoding (1426/1426 nt) | IS4 | repeat region | |||||
| * | ? | NC_000913 | = 4612024 | 105 (0.970) | 3 (0.030) | 3/524 | NT | 2.8% | intergenic (+23/‑104) | osmY/ytjA | salt‑inducible putative ABC transporter periplasmic binding protein/uncharacterized protein |
| ? | NC_000913 | = 4612030 | 108 (1.030) | intergenic (+29/‑98) | osmY/ytjA | salt‑inducible putative ABC transporter periplasmic binding protein/uncharacterized protein | |||||