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 | 188,837 | C→T | R316C (CGC→TGC) | PP_0165 → | GGDEF domain‑containing protein |
| RA | 233,545 | C→T | G548G (GGC→GGT) | PP_0180 → | cytochrome c family protein |
| RA | 476,133 | A→T | Q141L (CAG→CTG) | tsaD → | tRNA N6‑adenosine(37)‑threonylcarbamoyltransferase complex transferase subunit TsaD |
| RA | 1,011,323 | +T | intergenic (‑258/+192) | PP_0871 ← / ← SBRG_Ecoli_galM | glycine betaine/carnitine/choline ABC transporter permease/SBRG_Ecoli_galM |
| RA | 1,167,912 | +A | coding (725/1344 nt) | oprB‑I → | carbohydrate‑selective porin |
| MC JC | 1,515,811 | (33-bp)2→1 | pseudogene (715‑747/1851 nt) | PP_1325 ← | putative lipoprotein |
| RA | 1,856,513 | A→G | D203G (GAT→GGT) | relA → | ATP:GTP 3'‑pyrophosphotransferase |
| RA | 4,018,201 | G→A | intergenic (+144/‑36) | mvaB → / → PP_mr44 | hydroxymethylglutaryl‑CoA lyase/CrcZ ncRNA |
| RA | 4,746,222 | +C | intergenic (+464/+288) | gltA → / ← yeiW | citrate synthase/putative oxidoreductase |
| RA | 4,746,224 | A→G | intergenic (+466/+286) | gltA → / ← yeiW | citrate synthase/putative oxidoreductase |
| RA | 4,746,226 | C→T | intergenic (+468/+284) | gltA → / ← yeiW | citrate synthase/putative oxidoreductase |
| RA | 4,746,229 | C→T | intergenic (+471/+281) | gltA → / ← yeiW | citrate synthase/putative oxidoreductase |
| RA | 4,746,232 | C→G | intergenic (+474/+278) | gltA → / ← yeiW | citrate synthase/putative oxidoreductase |
| RA | 4,746,234 | 2 bp→CT | intergenic (+476/+275) | gltA → / ← yeiW | citrate synthase/putative oxidoreductase |
| RA | 4,746,248 | C→T | intergenic (+490/+262) | gltA → / ← yeiW | citrate synthase/putative oxidoreductase |
| RA | 4,746,250 | A→C | intergenic (+492/+260) | gltA → / ← yeiW | citrate synthase/putative oxidoreductase |
| RA | 4,746,253 | 2 bp→GC | intergenic (+495/+256) | gltA → / ← yeiW | citrate synthase/putative oxidoreductase |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_002947 | 171375–176275 | 176275 | 1–4901 | 6 [5] | [5] 6 | PP_16SA–[PP_5SA] | PP_16SA,PP_23SA,[PP_5SA] |
| * | * | ÷ | NC_002947 | 176678–181679 | 181679 | 1–5002 | 6 [2] | [5] 6 | PP_16SB–[PP_r01] | PP_16SB,PP_23SB,[PP_r01] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_002947 | 336209 = | 11 (0.410) | 4 (0.180) | 3/240 | 2.9 | 32.0% | intergenic (+54/+339) | PP_0278/PP_0279 | hypothetical protein/hypothetical protein |
| ? | NC_002947 | 336329 = | 8 (0.360) | intergenic (+174/+219) | PP_0278/PP_0279 | hypothetical protein/hypothetical protein | |||||
| * | ? | NC_002947 | 478264 = | 17 (0.630) | 3 (0.140) | 3/234 | 2.8 | 21.8% | intergenic (+9/+101) | PP_0393/cca | 2‑amino‑4‑hydroxy‑6‑ hydroxymethyldihydropteridine pyrophosphokinase/multifunctional tRNA nucleotidyltransferase/2',3'‑cyclic phosphodiesterase/2' nucleotidase/phosphatase |
| ? | NC_002947 | 478359 = | 8 (0.370) | intergenic (+104/+6) | PP_0393/cca | 2‑amino‑4‑hydroxy‑6‑ hydroxymethyldihydropteridine pyrophosphokinase/multifunctional tRNA nucleotidyltransferase/2',3'‑cyclic phosphodiesterase/2' nucleotidase/phosphatase | |||||
| * | ? | NC_002947 | 742918 = | NA (NA) | 7 (0.270) | 6/282 | 2.2 | NA | coding (1016/1422 nt) | PP_0635 | group II intron‑encoding maturase |
| ? | NC_002947 | 742948 = | NA (NA) | coding (1046/1422 nt) | PP_0635 | group II intron‑encoding maturase | |||||
| * | ? | NC_002947 | 1015848 = | 0 (0.000) | 30 (1.120) | 25/292 | 0.1 | 67.4% | intergenic (‑75/‑693) | SBRG_Ecoli_galE/prfC | SBRG_Ecoli_galE/peptide chain release factor 3 |
| ? | NC_002947 | 5066251 = | 29 (1.080) | intergenic (‑421/‑70) | PP_4458/PP_4459 | opine ABC transporter substrate‑binding protein/transposase | |||||
| * | ? | NC_002947 | = 1015854 | 1 (0.040) | 19 (0.730) | 18/284 | 0.4 | 66.7% | intergenic (‑81/‑687) | SBRG_Ecoli_galE/prfC | SBRG_Ecoli_galE/peptide chain release factor 3 |
| ? | NC_002947 | = 5067412 | 18 (0.690) | coding (1092/1098 nt) | PP_4459 | transposase | |||||
| * | ? | NC_002947 | 1154932 = | 20 (0.740) | 6 (0.240) | 5/270 | 2.4 | 29.7% | intergenic (‑224/+33) | PP_1008/gapA | RNA polymerase subunit sigma‑24/glyceraldehyde‑3‑phosphate dehydrogenase |
| ? | NC_002947 | = 2076208 | 10 (0.400) | intergenic (+168/+59) | PP_1846/PP_1847 | group II intron‑encoding maturase/TonB‑dependent ferric siderophore receptor | |||||
| * | ? | NC_002947 | 1424502 = | 5 (0.180) | 5 (0.240) | 3/230 | 2.8 | 50.2% | intergenic (‑36/+101) | PP_1242/PP_1244 | hypothetical protein/hypothetical protein |
| ? | NC_002947 | 1424596 = | 6 (0.280) | intergenic (‑130/+7) | PP_1242/PP_1244 | hypothetical protein/hypothetical protein | |||||
| * | ? | NC_002947 | = 1424533 | 5 (0.180) | 7 (0.330) | 3/230 | 2.8 | 58.6% | intergenic (‑67/+70) | PP_1242/PP_1244 | hypothetical protein/hypothetical protein |
| ? | NC_002947 | = 1424563 | 6 (0.280) | intergenic (‑97/+40) | PP_1242/PP_1244 | hypothetical protein/hypothetical protein | |||||
| * | ? | NC_002947 | 1491962 = | 21 (0.780) | 4 (0.190) | 3/234 | 2.8 | 23.7% | intergenic (+22/+108) | yhdZ/degS | amino acid ABC transporter ATP‑binding protein/serine endoprotease DegS |
| ? | NC_002947 | 1492052 = | 9 (0.420) | intergenic (+112/+18) | yhdZ/degS | amino acid ABC transporter ATP‑binding protein/serine endoprotease DegS | |||||
| * | ? | NC_002947 | 1504392 = | 13 (0.480) | 5 (0.220) | 4/248 | 2.6 | 38.5% | intergenic (+13/‑153) | trpS/zapE | tryptophan‑‑tRNA ligase/nucleoside triphosphate hydrolase domain‑containing protein |
| ? | NC_002947 | 1504475 = | 5 (0.220) | intergenic (+96/‑70) | trpS/zapE | tryptophan‑‑tRNA ligase/nucleoside triphosphate hydrolase domain‑containing protein | |||||
| * | ? | NC_002947 | = 1972169 | 6 (0.220) | 3 (0.140) | 3/228 | 2.8 | 26.5% | intergenic (+47/+72) | PP_1762/yciK | hypothetical protein/putative oxidoreductase |
| ? | NC_002947 | = 1972199 | 12 (0.570) | intergenic (+77/+42) | PP_1762/yciK | hypothetical protein/putative oxidoreductase | |||||
| * | ? | NC_002947 | = 2062815 | 13 (0.480) | 3 (0.130) | 3/246 | 3.0 | 20.1% | intergenic (+39/+89) | PP_1832/PP_1833 | oxidase/hypothetical protein |
| ? | NC_002947 | = 2062855 | 13 (0.570) | intergenic (+79/+49) | PP_1832/PP_1833 | oxidase/hypothetical protein | |||||
| * | ? | NC_002947 | = 2091242 | NA (NA) | 4 (0.160) | 4/278 | 2.9 | NA | coding (365/1302 nt) | PP_1865 | transposase |
| ? | NC_002947 | = 2091288 | NA (NA) | coding (411/1302 nt) | PP_1865 | transposase | |||||
| * | ? | NC_002947 | = 2241926 | 16 (0.590) | 5 (0.210) | 5/262 | 2.4 | 28.4% | intergenic (+29/+99) | uvrB/PP_1975 | uvrABC excinuclease protein B/EmrB/QacA family drug resistance transporter |
| ? | NC_002947 | = 2241985 | 11 (0.460) | intergenic (+88/+40) | uvrB/PP_1975 | uvrABC excinuclease protein B/EmrB/QacA family drug resistance transporter | |||||
| * | ? | NC_002947 | 2477094 = | 6 (0.220) | 3 (0.150) | 3/216 | 2.6 | 48.4% | intergenic (+6/+143) | PP_2166/PP_2167 | anti‑anti‑sigma factor/PhoD‑like phosphatase |
| ? | NC_002947 | 2477218 = | 2 (0.100) | intergenic (+130/+19) | PP_2166/PP_2167 | anti‑anti‑sigma factor/PhoD‑like phosphatase | |||||
| * | ? | NC_002947 | = 2799902 | 23 (0.850) | 8 (0.300) +T |
6/292 | 2.3 | 24.4% | intergenic (+18/+94) | PP_2447/puuB | hypothetical protein/gamma‑glutamylputrescine oxidase |
| ? | NC_002947 | = 2799976 | 27 (1.000) | intergenic (+92/+20) | PP_2447/puuB | hypothetical protein/gamma‑glutamylputrescine oxidase | |||||
| * | ? | NC_002947 | 4164076 = | 23 (0.850) | 7 (0.290) | 4/262 | 2.7 | 31.5% | intergenic (+31/‑178) | PP_3661/PP_3662 | membrane protein/hypothetical protein |
| ? | NC_002947 | 4164136 = | 10 (0.410) | intergenic (+91/‑118) | PP_3661/PP_3662 | membrane protein/hypothetical protein | |||||
| * | ? | NC_002947 | 4529388 = | 18 (0.670) | 7 (0.290) | 5/266 | 2.4 | 31.6% | intergenic (+18/‑175) | idh/PP_4013 | isocitrate dehydrogenase/MutT/nudix family protein |
| ? | NC_002947 | 4529423 = | 14 (0.570) | intergenic (+53/‑140) | idh/PP_4013 | isocitrate dehydrogenase/MutT/nudix family protein | |||||
| * | ? | NC_002947 | 4591012 = | 11 (0.410) | 5 (0.250) | 5/218 | 1.9 | 49.6% | intergenic (+102/+115) | PP_4061/PP_4063 | hypothetical protein/long‑chain fatty acid‑‑CoA ligase |
| ? | NC_002947 | 4591116 = | 2 (0.100) | intergenic (+206/+11) | PP_4061/PP_4063 | hypothetical protein/long‑chain fatty acid‑‑CoA ligase | |||||
| * | ? | NC_002947 | 4652552 = | 2 (0.070) | 4 (0.200) | 3/216 | 2.6 | 51.7% | intergenic (+10/+121) | fusB/PP_4112 | elongation factor G 2/sulfate transporter |
| ? | NC_002947 | 4652660 = | 6 (0.300) | intergenic (+118/+13) | fusB/PP_4112 | elongation factor G 2/sulfate transporter | |||||
| * | ? | NC_002947 | = 4652590 | 2 (0.070) | 6 (0.300) | 5/216 | 1.9 | 61.6% | intergenic (+48/+83) | fusB/PP_4112 | elongation factor G 2/sulfate transporter |
| ? | NC_002947 | = 4652620 | 6 (0.300) | intergenic (+78/+53) | fusB/PP_4112 | elongation factor G 2/sulfate transporter | |||||
| * | ? | NC_002947 | 4813167 = | 0 (0.000) | 6 (0.220) | 4/290 | 3.0 | 38.7% | intergenic (‑282/‑273) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947 | = 4950366 | 19 (0.710) | intergenic (+732/+66) | PP_5673/flhB | D‑alanine‑‑D‑alanine ligase/flagellin export apparatus substrate specificity protein | |||||
| * | ? | NC_002947 | = 4813173 | 2 (0.070) | 13 (0.520) | 11/270 | 1.1 | 52.2% | intergenic (‑288/‑267) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947 | 5993770 = | 22 (0.890) | intergenic (+59/‑487) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947 | 5133802 = | 18 (0.670) | 6 (0.230) | 5/278 | 2.5 | 27.3% | coding (300/438 nt) | PP_4515 | MarR family transcriptional regulator |
| ? | NC_002947 | 5133835 = | 15 (0.590) | coding (267/438 nt) | PP_4515 | MarR family transcriptional regulator | |||||
| * | ? | NC_002947 | 5316377 = | NA (NA) | 5 (0.190) | 4/280 | 2.9 | 100% | noncoding (1302/1522 nt) | PP_16SG | 16S ribosomal RNA |
| ? | NC_002947 | 5316385 = | 0 (0.000) | noncoding (1294/1522 nt) | PP_16SG | 16S ribosomal RNA | |||||
| * | ? | NC_002947 | = 5387429 | 10 (0.370) | 4 (0.190) | 3/224 | 2.7 | 32.5% | intergenic (+52/+81) | smpB/pdhR | SsrA‑binding protein/DNA‑binding transcriptional regulator LldR |
| ? | NC_002947 | = 5387457 | 9 (0.440) | intergenic (+80/+53) | smpB/pdhR | SsrA‑binding protein/DNA‑binding transcriptional regulator LldR | |||||
| * | ? | NC_002947 | = 5660597 | 19 (0.700) | 6 (0.230) | 5/280 | 2.5 | 21.4% | intergenic (‑52/+100) | epd/tktA | D‑erythrose 4‑phosphate dehydrogenase/transketolase A |
| ? | NC_002947 | = 5660674 | 26 (1.010) | intergenic (‑129/+23) | epd/tktA | D‑erythrose 4‑phosphate dehydrogenase/transketolase A | |||||
| * | ? | NC_002947 | 5739035 = | 16 (0.590) | 6 (0.240) | 6/270 | 2.1 | 29.5% | intergenic (‑56/+101) | proY/hutH | proline (histidine) APC transporter/histidine ammonia‑lyase |
| ? | NC_002947 | 5739114 = | 14 (0.560) | intergenic (‑135/+22) | proY/hutH | proline (histidine) APC transporter/histidine ammonia‑lyase | |||||
| * | ? | NC_002947 | 5748341 = | 12 (0.440) | 10 (0.410) | 5/268 | 2.4 | 52.7% | intergenic (‑169/+78) | fbp/glgP | class 1 fructose‑1,6‑bisphosphatase/glycogen phosphorylase |
| ? | NC_002947 | 5748395 = | 7 (0.280) | intergenic (‑223/+24) | fbp/glgP | class 1 fructose‑1,6‑bisphosphatase/glycogen phosphorylase | |||||
| * | ? | NC_002947 | 5821859 = | 16 (0.590) | 6 (0.250) | 5/258 | 2.3 | 32.4% | intergenic (+40/+89) | PP_5092/pilT | NLP/P60 protein/twitching motility protein |
| ? | NC_002947 | 5821922 = | 11 (0.460) | intergenic (+103/+26) | PP_5092/pilT | NLP/P60 protein/twitching motility protein | |||||
| * | ? | NC_002947 | 5919162 = | 13 (0.480) | 5 (0.230) | 3/238 | 2.9 | 29.0% | intergenic (+49/+104) | spuI/argA | glutamylpolyamine synthetase/amino acid N‑acetyltransferase |
| ? | NC_002947 | 5919258 = | 14 (0.640) | intergenic (+145/+8) | spuI/argA | glutamylpolyamine synthetase/amino acid N‑acetyltransferase | |||||
| * | ? | NC_002947 | = 6005937 | 11 (0.410) | 3 (0.140) | 3/234 | 2.8 | 21.6% | intergenic (+39/+70) | PP_5256/amaA | cyclic nucleotide‑binding protein/L‑pipecolate oxidase |
| ? | NC_002947 | = 6005971 | 13 (0.600) | intergenic (+73/+36) | PP_5256/amaA | cyclic nucleotide‑binding protein/L‑pipecolate oxidase | |||||