mutation predictions | marginal predictions | summary statistics | genome diff | command line log
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breseq version 0.33.1 revision 8505477f25b3
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Predicted mutations | |||||
|---|---|---|---|---|---|
| evidence | position | mutation | annotation | gene | description |
| RA | 312,546 | G→T | intergenic (‑80/‑1035) | b4671 ← / → yeeJ_2 | Gene added/attaching and effacing protein |
| RA | 547,694 | A→G | intergenic (+123/‑1156) | fdrA → / → ylbF | acyl‑CoA synthetase with NAD(P)‑bindingRossmann‑fold domain/hypothetical protein |
| RA | 547,835 | +G | intergenic (+264/‑1015) | fdrA → / → ylbF | acyl‑CoA synthetase with NAD(P)‑bindingRossmann‑fold domain/hypothetical protein |
| RA | 556,858 | A→T | L36Q (CTG→CAG) | folD ← | bifunctional 5,10‑methylene‑tetrahydrofolatedehydrogenase/5,10‑methylene ‑tetrahydrofolatecyclohydrolase |
| MC JC | 654,214 | Δ1,199 bp | insH_12 | insH_12 | |
| RA | 987,574 | G→T | intergenic (‑170/+433) | ompF ← / ← asnS | outer membrane porin 1a (Ia;b;F)/asparaginyl tRNA synthetase |
| RA | 1,093,686 | T→C | V130A (GTA→GCA) | ycdT → | diguanylate cyclase |
| RA | 1,197,797 | C→T | H366H (CAC→CAT) | icd → | isocitrate dehydrogenase,‑specific for NADP+ |
| RA | 1,197,809 | C→T | T370T (ACC→ACT) | icd → | isocitrate dehydrogenase,‑specific for NADP+ |
| RA | 1,197,822 | T→C | L375M (TTA→CTG) | icd → | isocitrate dehydrogenase,‑specific for NADP+ |
| RA | 1,197,824 | A→G | L375M (TTA→CTG) | icd → | isocitrate dehydrogenase,‑specific for NADP+ |
| RA | 1,197,854 | C→T | N385N (AAC→AAT) | icd → | isocitrate dehydrogenase,‑specific for NADP+ |
| MC JC | 1,301,041 | Δ1,336 bp | insC_8–insD_10 | insC_8, insD_10 | |
| RA | 1,519,222 | G→T | V40V (GTG→GTT) | ydcX → | inner membrane protein |
| RA | 1,669,601 | Δ1 bp | coding (678/1221 nt) | dgsA ← | DNA‑binding transcriptional repressor |
| RA | 1,979,957 | G→T | intergenic (‑37/+398) | flhD ← / ← insH_10 | DNA‑binding transcriptional dual regulator/IS5 element protein |
| RA | 2,005,401 | C→T | E115K (GAA→AAA) | fliC ← | flagellar filament structural protein |
| RA | 2,074,160 | C→A | A162E (GCG→GAG) | flu → | antigen 43 (Ag43) phase‑variable biofilmformation autotransporter |
| MC JC | 2,176,983 | Δ1,199 bp | insH_11 | insH_11 | |
| RA | 2,245,455 | A→G | S283P (TCG→CCG) | yeiB ← | inner membrane protein |
| RA | 2,253,783 | G→T | A245S (GCG→TCG) | yeiH → | inner membrane protein |
| JC | 2,288,259 | (TTATCGCCT)2→3 | coding (550/1761 nt) | yejM → | hydrolase, inner membrane |
| MC JC | 2,320,795 | Δ1,336 bp | insD_9–insC_5 | insD_9, insC_5 | |
| RA | 2,866,111 | A→G | intergenic (‑21/+159) | rpoS ← / ← nlpD | RNA polymerase, sigma S (sigma 38) factor/outer membrane lipoprotein |
| RA | 2,935,326 | C→A | R363S (CGT→AGT) | fucI → | L‑fucose isomerase |
| RA | 3,045,138 | T→C | T854A (ACG→GCG) | gcvP ← | glycine decarboxylase, PLP‑dependent, subunit(protein P) of glycine cleavage complex |
| MC JC | 3,261,134 | Δ1,199 bp | insH_16–[tdcD] | insH_16, [tdcD] | |
| RA | 3,268,825 | A→G | T186A (ACA→GCA) | yhaC → | hypothetical protein |
| RA | 3,423,631 | G→T | noncoding (12/120 nt) | rrfD ← | 5S ribosomal RNA |
| RA | 3,453,401 | G→A | A679V (GCA→GTA) | rpoB ← | RNA polymerase subunit beta |
| RA | 3,542,160 | A→G | intergenic (+202/‑249) | rhaA → / → rhaD | L‑rhamnose isomerase/rhamnulose‑1‑phosphate aldolase |
| RA | 3,542,162 | A→G | intergenic (+204/‑247) | rhaA → / → rhaD | L‑rhamnose isomerase/rhamnulose‑1‑phosphate aldolase |
| RA | 3,542,165 | T→C | intergenic (+207/‑244) | rhaA → / → rhaD | L‑rhamnose isomerase/rhamnulose‑1‑phosphate aldolase |
| RA | 3,542,182 | A→G | intergenic (+224/‑227) | rhaA → / → rhaD | L‑rhamnose isomerase/rhamnulose‑1‑phosphate aldolase |
| RA | 3,542,266 | A→C | intergenic (+308/‑143) | rhaA → / → rhaD | L‑rhamnose isomerase/rhamnulose‑1‑phosphate aldolase |
| MC JC | 3,742,936 | Δ1,336 bp | insD_8–insC | insD_8, insC | |
| MC JC | 3,746,911 | Δ1,199 bp | insH_13 | insH_13 | |
| MC JC | 3,750,591 | Δ1,199 bp | insH_14 | insH_14 | |
| MC JC | 3,958,123 | Δ34 bp | coding (1156‑1189/1287 nt) | dctA → | C4‑dicarboxylic acid, orotate and citratetransporter |
| RA | 4,255,957 | G→T | intergenic (+84/‑139) | yjbI → / → ubiC | hypothetical protein/chorismate pyruvate lyase |
| MC JC | 4,310,363 | Δ1,199 bp | insH_15–[alsK] | insH_15, [alsK] | |
| RA | 4,371,274 | (A)5→3 | intergenic (‑9/+296) | dcuA ← / ← aspA | C4‑dicarboxylate antiporter/aspartate ammonia‑lyase |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_007779_cfb | 1197857 | 1213066 | 15210 | 53 [51] | [49] 52 | [icd]–mcrA | [icd],ymfD,ymfE,lit,intE,xisE,ymfH,ymfI,ymfJ,cohE,croE,ymfL,ymfM,ymfN,ymfR,ymfO,ymfP,ymfQ,stfP,tfaP,tfaE,pinE,mcrA |
| * | * | ÷ | NC_007779_cfb | 1395926 | 1398820–1397761 | 1836–2895 | 148 [1] | [51] 53 | [mppA]–insH_8 | [mppA],ynaI,insH_8 |
| * | * | ÷ | NC_007779_cfb | 3423644–3426507 | 3426507 | 1–2864 | 56 [51] | [51] 52 | [rrlD] | [rrlD] |
| * | * | ÷ | NC_007779_cfb | 3597406–3597978 | 3601369–3600948 | 2971–3964 | 52 [51] | [50] 52 | [rrlA]–rrsA | [rrlA],alaT,ileT,rrsA |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_007779_cfb | 380484 = | NA (NA) | 113 (0.960) | 99/432 | 0.3 | NA | intergenic (‑418/‑46) | yaiO/insC_2 | hypothetical protein/IS2 insertion element repressor InsA |
| ? | NC_007779_cfb | = 381407 | NA (NA) | coding (510/906 nt) | insD | IS2 insertion element transposase InsAB' | |||||
| * | ? | NC_007779_cfb | 381401 = | NA (NA) | 124 (1.070) | 109/428 | 0.1 | NA | coding (504/906 nt) | insD | IS2 insertion element transposase InsAB' |
| ? | NC_007779_cfb | = 381812 | NA (NA) | coding (303/387 nt) | yaiF | hypothetical protein | |||||
| * | ? | NC_007779_cfb | = 1395925 | 1 (0.010) | 118 (1.020) | 97/426 | 0.3 | 99.2% | coding (985/1614 nt) | mppA | murein tripeptide(L‑ala‑gamma‑D‑glutamyl‑meso‑DAP) transporter subunit |
| ? | NC_007779_cfb | 1397761 = | NA (NA) | intergenic (‑125/‑29) | ynaI/insH_8 | inner membrane protein/IS5 transposase and trans‑activator | |||||
| * | ? | NC_007779_cfb | 2316870 = | 7 (0.060) | 120 (1.040) | 96/424 | 0.3 | 94.6% | coding (49/2673 nt) | rcsD | phosphotransfer intermediate protein intwo‑component regulatory system with RcsBC |
| ? | NC_007779_cfb | 2519723 = | NA (NA) | intergenic (+33/‑54) | nupC/insL | nucleoside (except guanosine) transporter/transposase | |||||
| * | ? | NC_007779_cfb | = 2316881 | 3 (0.030) | 150 (1.290) | 132/428 | 0.0 | 98.1% | coding (60/2673 nt) | rcsD | phosphotransfer intermediate protein intwo‑component regulatory system with RcsBC |
| ? | NC_007779_cfb | = 2521059 | NA (NA) | intergenic (+170/+30) | insL/yfeA | transposase/diguanylate cyclase | |||||
| * | ? | NC_007779_cfb | = 3186081 | NA (NA) | 108 (0.930) | 91/430 | 0.4 | 99.1% | coding (26/2466 nt) | yqiG | outer membrane usher protein |
| ? | NC_007779_cfb | 3512753 = | 1 (0.010) | coding (529/1026 nt) | cytR | DNA‑binding transcriptional dual regulator | |||||
| * | ? | NC_007779_cfb | = 3512759 | 3 (0.030) | 81 (0.690) | 74/430 | 1.0 | 96.4% | coding (535/1026 nt) | cytR | DNA‑binding transcriptional dual regulator |
| ? | NC_007779_cfb | = 3744262 | NA (NA) | intergenic (‑90/+31) | insC/yidZ | IS2 element protein/DNA‑binding transcriptional regulator | |||||
| * | ? | NC_007779_cfb | = 3744263 | NA (NA) | 126 (1.080) | 103/432 | 0.2 | 98.4% | intergenic (‑91/+30) | insC/yidZ | IS2 element protein/DNA‑binding transcriptional regulator |
| ? | NC_007779_cfb | 3903274 = | 2 (0.020) | coding (37/825 nt) | bax | hypothetical protein | |||||
| * | ? | NC_007779_cfb | = 3903279 | 7 (0.060) | 162 (1.390) | 131/430 | 0.0 | 95.9% | coding (42/825 nt) | bax | hypothetical protein |
| ? | NC_007779_cfb | = 4504190 | NA (NA) | intergenic (+10/‑89) | insD_3/yjgW | IS2 insertion element transposase InsAB'/hypothetical protein | |||||
| * | ? | NC_007779_cfb | = 3988378 | NA (NA) | 166 (1.420) | 129/430 | 0.0 | 98.8% | coding (747/783 nt) | yhiS | hypothetical protein |
| ? | NC_007779_cfb | = 4365922 | 2 (0.020) | coding (691/1539 nt) | cadC | DNA‑binding transcriptional activator | |||||
| * | ? | NC_007779_cfb | 4310363 = | NA (NA) | 196 (1.670) | 133/432 | 0.0 | 100% | intergenic (‑287/‑68) | yjcS/insH_15 | alkyl sulfatase/IS5 element protein |
| ? | NC_007779_cfb | = 4342649 | 0 (0.000) | intergenic (‑42/+283) | adiY/adiA | DNA‑binding transcriptional activator/biodegradative arginine decarboxylase | |||||
| * | ? | NC_007779_cfb | 4310363 = | NA (NA) | 121 (1.030) | 103/432 | 0.2 | 99.2% | intergenic (‑287/‑68) | yjcS/insH_15 | alkyl sulfatase/IS5 element protein |
| ? | NC_007779_cfb | 4365918 = | 1 (0.010) | coding (695/1539 nt) | cadC | DNA‑binding transcriptional activator | |||||
| * | ? | NC_007779_cfb | = 4311556 | NA (NA) | 161 (1.380) | 103/430 | 0.2 | 97.6% | coding (922/1029 nt) | alsK | D‑allose kinase |
| ? | NC_007779_cfb | 4540915 = | 4 (0.030) | intergenic (+204/+379) | yjhR/nanS | frameshift suppressor/hypothetical protein | |||||
| * | ? | NC_007779_cfb | = 4311557 | NA (NA) | 87 (0.740) | 72/432 | 1.2 | 96.7% | coding (921/1029 nt) | alsK | D‑allose kinase |
| ? | NC_007779_cfb | 4342646 = | 3 (0.030) | intergenic (‑39/+286) | adiY/adiA | DNA‑binding transcriptional activator/biodegradative arginine decarboxylase | |||||