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 |
| MC JC | 257,908 | Δ776 bp | 100% | [crl] | [crl] | |
| RA | 451,643 | G→A | 76.7% | intergenic (‑33/+427) | cyoA ← / ← ampG | cytochrome o ubiquinol oxidase subunit II/muropeptide transporter |
| RA | 652,453 | G→A | 5.4% | A73A (GCG→GCA) | citA → | sensory histidine kinase in two‑component regulatory system with CitB |
| JC JC | 1,293,032 | IS1 (–) +8 bp | 100% | intergenic (‑110/‑488) | 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 | 1,902,141 | G→A | 5.2% | G32S (GGC→AGC) | manX → | fused mannose‑specific PTS enzymes: IIA component/IIB component |
| MC JC | 1,978,503 | Δ776 bp | 100% | insB1–insA | insB1, insA | |
| JC JC | 1,979,486 | IS5 (+) +4 bp | 100% | intergenic (‑271/‑264) | insA ← / → uspC | IS1 repressor TnpA/universal stress protein |
| RA | 2,132,787 | A→C | 100% | I204S (ATC→AGC) | wcaA ← | putative glycosyl transferase |
| 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 | 2,202,096 | G→A | 8.8% | A606A (GCG→GCA) | yehI → | DUF4132 domain‑containing protein |
| RA | 2,241,663:1 | +A | 5.3% | coding (6/1041 nt) | galS ← | galactose‑ and fucose‑inducible galactose regulon transcriptional isorepressor; mgl operon transcriptional repressor; autorepressor |
| RA | 2,304,680 | T→C | 9.0% | intergenic (+287/+428) | eco → / ← mqo | ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain |
| JC JC | 2,876,678 | IS5 (+) +4 bp | 9.1% | coding (98‑101/1038 nt) | iap → | aminopeptidase in alkaline phosphatase isozyme conversion |
| RA | 3,065,956 | A→G | 8.3% | E385E (GAA→GAG) | scpC → | propionyl‑CoA:succinate CoA transferase |
| 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 |
| MC JC | 3,815,859 | Δ82 bp | 100% | [rph]–[rph] | [rph], [rph] | |
| RA | 3,951,598:1 | +A | 6.1% | pseudogene (57/663 nt) | ilvG → | pseudogene, acetolactate synthase 2 large subunit, valine‑insensitive; acetolactate synthase II, large subunit, cryptic, interrupted |
| JC | 3,968,508 | Δ12 bp | 10.9% | coding (593‑604/1104 nt) | wecA → | UDP‑GlcNAc:undecaprenylphosphate GlcNAc‑1‑phosphate transferase |
| JC | 3,968,671 | Δ9 bp | 5.5% | coding (756‑764/1104 nt) | wecA → | UDP‑GlcNAc:undecaprenylphosphate GlcNAc‑1‑phosphate transferase |
| MC JC | 4,001,645 | Δ5 bp | 100% | coding (220‑224/951 nt) | corA → | magnesium/nickel/cobalt transporter |
| RA | 4,184,543 | C→A | 100% | P1100Q (CCG→CAG) | rpoB → | RNA polymerase, beta subunit |
| RA | 4,296,060 | C→T | 10.7% | intergenic (+266/+376) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,190 | A→G | 22.6% | intergenic (+396/+246) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,191 | A→C | 35.2% | intergenic (+397/+245) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,268 | T→C | 26.5% | intergenic (+474/+168) | 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 | 4,544,444 | T→C | 9.5% | Y47Y (TAT→TAC) | fimC → | periplasmic chaperone |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 2469044 | 2469914 | 871 | 22 [20] | [21] 22 | [gtrB]–[gtrS] | [gtrB],[gtrS] |
| * | * | ÷ | NC_000913 | 2785998 | 2786712 | 715 | 22 [20] | [21] 23 | [ygaQ] | [ygaQ] |
| * | * | ÷ | NC_000913 | 2994961 | 2995477 | 517 | 23 [21] | [20] 25 | [ygeK]–[ygeN] | [ygeK],[ygeN] |
| * | * | ÷ | NC_000913 | 3287076 | 3287429 | 354 | 23 [21] | [19] 23 | [yraH] | [yraH] |
| * | * | ÷ | NC_000913 | 3360769 | 3361279 | 511 | 23 [21] | [21] 23 | [gltF] | [gltF] |
| * | * | ÷ | NC_000913 | 3423894–3424231 | 3424397–3424239 | 9–504 | 23 [21] | [21] 22 | rrlD | 23S ribosomal RNA of rrnD operon |
| * | * | ÷ | NC_000913 | 3581681 | 3582198 | 518 | 24 [18] | [20] 22 | [yhhZ] | [yhhZ] |
| * | * | ÷ | NC_000913 | 3769554 | 3770078 | 525 | 22 [20] | [17] 23 | [yibV]–[yibU] | [yibV],yibV,yibU,[yibU] |
| * | * | ÷ | NC_000913 | 3798636 | 3799653 | 1018 | 23 [21] | [19] 22 | [waaU]–[waaZ] | [waaU],[waaZ] |
| * | * | ÷ | NC_000913 | 4268445 | 4268725 | 281 | 22 [21] | [21] 25 | tyrB/yjbS | tyrosine aminotransferase, tyrosine‑repressible, PLP‑dependent/uncharacterized protein |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 224910 = | NA (NA) | 5 (0.070) | 4/498 | NT | NA | noncoding (1140/1542 nt) | rrsH | 16S ribosomal RNA of rrnH operon |
| ? | NC_000913 | 225157 = | NA (NA) | noncoding (1387/1542 nt) | rrsH | 16S ribosomal RNA of rrnH operon | |||||
| * | ? | NC_000913 | = 243009 | 91 (1.150) | 5 (0.070) | 3/500 | NT | 5.1% | coding (295/2445 nt) | fadE | acyl coenzyme A dehydrogenase |
| ? | NC_000913 | = 243192 | 96 (1.250) | coding (112/2445 nt) | fadE | acyl coenzyme A dehydrogenase | |||||
| * | ? | NC_000913 | 379965 = | 50 (0.630) | 4 (0.050) | 4/504 | NT | 7.0% | intergenic (‑84/+104) | frmR/yaiO | regulator protein that represses frmRAB operon/outer membrane protein |
| ? | NC_000913 | 380853 = | 58 (0.750) | pseudogene (408/417 nt) | yaiX | pseudogene, interrupted by IS2A; hexapeptide transferase superfamily; putative transferase | |||||
| * | ? | NC_000913 | 1207790 = | 35 (0.440) | 41 (0.550) | 29/482 | NT | 58.2% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | 1209619 = | 26 (0.350) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 32 (0.410) | 52 (0.700) | 44/482 | NT | 65.0% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | = 1209602 | 26 (0.350) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1731973 | 73 (0.930) | 4 (0.050) | 4/494 | NT | 5.5% | coding (2887/4617 nt) | lhr | putative ATP‑dependent helicase |
| ? | NC_000913 | = 1732058 | 66 (0.870) | coding (2972/4617 nt) | lhr | putative ATP‑dependent helicase | |||||
| * | ? | NC_000913 | 2270129 = | 92 (1.170) | 8 (0.100) | 8/514 | NT | 8.0% | coding (151/567 nt) | mepS | murein DD‑endopeptidase, space‑maker hydrolase, mutational suppressor of prc thermosensitivity, outer membrane lipoprotein, weak murein LD‑carboxypeptidase |
| ? | NC_000913 | = 2290113 | NA (NA) | noncoding (1/1195 nt) | IS5 | repeat region | |||||
| * | ? | NC_000913 | 2881790 = | 67 (0.850) | 4 (0.050) | 4/506 | NT | 7.4% | coding (353/1092 nt) | casC | CRISP RNA (crRNA) containing Cascade antiviral complex protein |
| ? | NC_000913 | 2882112 = | 34 (0.440) | coding (31/1092 nt) | casC | CRISP RNA (crRNA) containing Cascade antiviral complex protein | |||||
| * | ? | NC_000913 | = 3652919 | NA (NA) | 3 (0.040) | 3/506 | NT | 6.0% | noncoding (312/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 3655093 | 48 (0.610) | coding (411/531 nt) | dctR | Putative LuxR family repressor for dicarboxylate transport | |||||