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 | 1,844,126 | Δ1 bp | coding (710/2754 nt) | gacS ← | sensor protein GacS |
| RA | 1,852,105 | G→T | K383N (AAG→AAT) | relA → | ATP:GTP 3'‑pyrophosphotransferase |
| RA | 4,741,283 | C→G | intergenic (+474/+278) | gltA → / ← yeiW | citrate synthase/putative oxidoreductase |
| RA | 4,741,285 | 2 bp→CT | intergenic (+476/+275) | gltA → / ← yeiW | citrate synthase/putative oxidoreductase |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_002947 | 171377–172965 | 176327–172975 | 11–4951 | 5 [4] | [4] 7 | PP_16SA–[PP_5SA] | PP_16SA,PP_23SA,[PP_5SA] |
| * | * | ÷ | NC_002947 | 176674–178395 | 181715–178405 | 11–5042 | 5 [3] | [4] 5 | PP_16SB–[PP_r01] | PP_16SB,PP_23SB,[PP_r01] |
| * | * | ÷ | NC_002947 | 4808200 | 4808244 | 45 | 5 [4] | [4] 5 | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_002947 | = 176399 | NA (NA) | 12 (0.500) +CGAAA |
8/254 | 1.7 | 31.6% | intergenic (+43/‑420) | PP_5SA/PP_16SB | 5S ribosomal RNA/16S ribosomal RNA |
| ? | NC_002947 | = 182013 | 27 (1.090) | intergenic (+2/+63) | PP_5SB/PP_0160 | 5S ribosomal RNA/ferrioxamine receptor | |||||
| * | ? | NC_002947 | = 312731 | 22 (0.890) | 7 (0.320) | 7/236 | 1.7 | 24.7% | coding (483/831 nt) | fdhD | protein sulfur transferase |
| ? | NC_002947 | = 312759 | 23 (1.040) | coding (455/831 nt) | fdhD | protein sulfur transferase | |||||
| * | ? | NC_002947 | = 380858 | 20 (0.800) | 5 (0.240) | 5/218 | 2.1 | 21.1% | intergenic (+45/+64) | gbcB/PP_0317 | glycine‑betaine dioxygenase subunit/methyl‑accepting chemotaxis transducer |
| ? | NC_002947 | = 380892 | 21 (1.020) | intergenic (+79/+30) | gbcB/PP_0317 | glycine‑betaine dioxygenase subunit/methyl‑accepting chemotaxis transducer | |||||
| * | ? | NC_002947 | = 513455 | 16 (0.640) | 4 (0.170) | 4/246 | 2.7 | 22.3% | intergenic (‑99/‑92) | crp/yhfA | DNA‑binding transcriptional dual regulator/hypothetical protein |
| ? | NC_002947 | = 513472 | 13 (0.560) | intergenic (‑116/‑75) | crp/yhfA | DNA‑binding transcriptional dual regulator/hypothetical protein | |||||
| * | ? | NC_002947 | 1138537 = | 36 (1.450) | 7 (0.320) | 7/236 | 1.7 | 20.8% | intergenic (‑62/+103) | arcC/arcB | carbamate kinase/ornithine carbamoyltransferase |
| ? | NC_002947 | 1138626 = | 21 (0.950) | intergenic (‑151/+14) | arcC/arcB | carbamate kinase/ornithine carbamoyltransferase | |||||
| * | ? | NC_002947 | = 1228140 | 21 (0.850) | 6 (0.260) | 5/248 | 2.4 | 21.9% | coding (1314/4320 nt) | PP_1072 | leucine‑rich repeat‑containing protein |
| ? | NC_002947 | = 1228145 | 23 (0.990) | coding (1319/4320 nt) | PP_1072 | leucine‑rich repeat‑containing protein | |||||
| * | ? | NC_002947 | = 1421592 | 15 (0.600) | 4 (0.170) | 4/252 | 2.7 | 21.4% | coding (166/1860 nt) | PP_1246 | hypothetical protein |
| ? | NC_002947 | = 1421617 | 15 (0.630) | coding (191/1860 nt) | PP_1246 | hypothetical protein | |||||
| * | ? | NC_002947 | 1427331 = | NA (NA) | 5 (0.210) | 5/250 | 2.4 | NA | coding (1222/1422 nt) | PP_1250 | group II intron‑encoding maturase |
| ? | NC_002947 | 1427349 = | NA (NA) | coding (1240/1422 nt) | PP_1250 | group II intron‑encoding maturase | |||||
| * | ? | NC_002947 | = 1443135 | 17 (0.680) | 8 (0.400) | 8/214 | 1.3 | 32.8% | intergenic (‑66/+110) | ghrB/PP_1262 | 2‑ketoaldonate reductase/hydroxypyruvate/glyoxylate reductase/LysR family transcriptional regulator |
| ? | NC_002947 | = 1443153 | 19 (0.940) | intergenic (‑84/+92) | ghrB/PP_1262 | 2‑ketoaldonate reductase/hydroxypyruvate/glyoxylate reductase/LysR family transcriptional regulator | |||||
| * | ? | NC_002947 | 1487013 = | 28 (1.130) | 7 (0.360) | 6/204 | 1.6 | 30.0% | intergenic (+22/+108) | yhdZ/degS | amino acid ABC transporter ATP‑binding protein/serine endoprotease DegS |
| ? | NC_002947 | 1487103 = | 11 (0.570) | intergenic (+112/+18) | yhdZ/degS | amino acid ABC transporter ATP‑binding protein/serine endoprotease DegS | |||||
| * | ? | NC_002947 | = 1526707 | 19 (0.760) | 7 (0.300) | 7/246 | 1.8 | 27.6% | coding (852/957 nt) | ddlB | D‑alanine‑‑D‑alanine ligase B |
| ? | NC_002947 | = 1526720 | 19 (0.820) | coding (865/957 nt) | ddlB | D‑alanine‑‑D‑alanine ligase B | |||||
| * | ? | NC_002947 | = 1780127 | 19 (0.760) | 5 (0.240) | 5/226 | 2.1 | 21.6% | intergenic (+44/+62) | PP_1587/dapC | NhaP‑type Na+(K+)/H+ antiporter/N‑succinyl‑L,L‑diaminopimelate aminotransferase |
| ? | NC_002947 | = 1780151 | 20 (0.940) | intergenic (+68/+38) | PP_1587/dapC | NhaP‑type Na+(K+)/H+ antiporter/N‑succinyl‑L,L‑diaminopimelate aminotransferase | |||||
| * | ? | NC_002947 | 1967188 = | 13 (0.520) | 5 (0.270) | 5/198 | 1.8 | 31.5% | intergenic (+15/+104) | PP_1762/yciK | hypothetical protein/putative oxidoreductase |
| ? | NC_002947 | 1967284 = | 12 (0.640) | intergenic (+111/+8) | PP_1762/yciK | hypothetical protein/putative oxidoreductase | |||||
| * | ? | NC_002947 | = 2057866 | 20 (0.800) | 4 (0.200) | 4/216 | 2.4 | 20.3% | intergenic (+39/+89) | PP_1832/PP_1833 | oxidase/hypothetical protein |
| ? | NC_002947 | = 2057906 | 15 (0.740) | intergenic (+79/+49) | PP_1832/PP_1833 | oxidase/hypothetical protein | |||||
| * | ? | NC_002947 | 2063203 = | 26 (1.050) | 5 (0.250) | 5/214 | 2.0 | 25.6% | intergenic (+17/‑190) | PP_1838/PP_1839 | membrane protein/hypothetical protein |
| ? | NC_002947 | 2063297 = | 8 (0.400) | intergenic (+111/‑96) | PP_1838/PP_1839 | membrane protein/hypothetical protein | |||||
| * | ? | NC_002947 | 2271258 = | 24 (0.970) | 8 (0.370) | 7/232 | 1.7 | 29.0% | intergenic (+36/‑184) | PP_2002/PP_t31 | oxidoreductase/tRNA‑Val |
| ? | NC_002947 | 2271306 = | 18 (0.820) | intergenic (+84/‑136) | PP_2002/PP_t31 | oxidoreductase/tRNA‑Val | |||||
| * | ? | NC_002947 | = 2329471 | 24 (0.970) | 7 (0.300) | 5/250 | 2.4 | 23.8% | coding (1016/1239 nt) | PP_2047 | 3‑hydroxyacyl‑CoA dehydrogenase family protein |
| ? | NC_002947 | = 2329476 | 22 (0.930) | coding (1021/1239 nt) | PP_2047 | 3‑hydroxyacyl‑CoA dehydrogenase family protein | |||||
| * | ? | NC_002947 | = 3701419 | 16 (0.640) | 5 (0.210) | 4/254 | 2.7 | 21.6% | coding (116/1053 nt) | PP_3266 | hypothetical protein |
| ? | NC_002947 | = 3701458 | 21 (0.880) | coding (77/1053 nt) | PP_3266 | hypothetical protein | |||||
| * | ? | NC_002947 | 3920062 = | 15 (0.600) | 6 (0.250) | 6/258 | 2.2 | 26.9% | intergenic (+34/+59) | mobA/acs | molybdenum cofactor guanylyltransferase/acyl‑CoA synthetase |
| ? | NC_002947 | 3920118 = | 18 (0.740) | intergenic (+90/+3) | mobA/acs | molybdenum cofactor guanylyltransferase/acyl‑CoA synthetase | |||||
| * | ? | NC_002947 | 3968919 = | 8 (0.320) | 6 (0.250) | 5/256 | 2.4 | 28.7% | coding (1003/1179 nt) | PP_3498 | transposase |
| ? | NC_002947 | 3969010 = | 22 (0.910) | coding (1094/1179 nt) | PP_3498 | transposase | |||||
| * | ? | NC_002947 | 4021060 = | 19 (0.760) | 5 (0.210) | 5/254 | 2.4 | 21.1% | coding (1727/2067 nt) | PP_3546 | two‑component system sensor histidine kinase/response regulator |
| ? | NC_002947 | 4021082 = | 19 (0.790) | coding (1749/2067 nt) | PP_3546 | two‑component system sensor histidine kinase/response regulator | |||||
| * | ? | NC_002947 | 4524439 = | 22 (0.890) | 10 (0.450) | 8/236 | 1.5 | 34.1% | intergenic (+18/‑175) | idh/PP_4013 | isocitrate dehydrogenase/MutT/nudix family protein |
| ? | NC_002947 | 4524474 = | 19 (0.860) | intergenic (+53/‑140) | idh/PP_4013 | isocitrate dehydrogenase/MutT/nudix family protein | |||||
| * | ? | NC_002947 | 4586063 = | 5 (0.200) | 4 (0.230) | 4/188 | 2.0 | 54.9% | intergenic (+102/+115) | PP_4061/PP_4063 | hypothetical protein/long‑chain fatty acid‑‑CoA ligase |
| ? | NC_002947 | 4586167 = | 3 (0.170) | intergenic (+206/+11) | PP_4061/PP_4063 | hypothetical protein/long‑chain fatty acid‑‑CoA ligase | |||||
| * | ? | NC_002947 | = 4586100 | 5 (0.200) | 3 (0.170) | 3/188 | 2.4 | 47.8% | intergenic (+139/+78) | PP_4061/PP_4063 | hypothetical protein/long‑chain fatty acid‑‑CoA ligase |
| ? | NC_002947 | = 4586128 | 3 (0.170) | intergenic (+167/+50) | PP_4061/PP_4063 | hypothetical protein/long‑chain fatty acid‑‑CoA ligase | |||||
| * | ? | NC_002947 | = 4647641 | 7 (0.280) | 4 (0.230) | 4/186 | 2.0 | 40.1% | intergenic (+48/+83) | fusB/PP_4112 | elongation factor G 2/sulfate transporter |
| ? | NC_002947 | = 4647671 | 7 (0.400) | intergenic (+78/+53) | fusB/PP_4112 | elongation factor G 2/sulfate transporter | |||||
| * | ? | NC_002947 | 4726014 = | 27 (1.090) | 6 (0.250) | 6/250 | 2.1 | 21.6% | intergenic (‑136/+100) | PP_4183/brnQ | membrane protein/branched‑chain amino acid transporter |
| ? | NC_002947 | 4726042 = | 18 (0.760) | intergenic (‑164/+72) | PP_4183/brnQ | membrane protein/branched‑chain amino acid transporter | |||||
| * | ? | NC_002947 | = 5201663 | 14 (0.560) | 7 (0.390) | 5/190 | 1.8 | 38.8% | intergenic (‑101/‑79) | PP_4582/PP_4583 | membrane protein/putative Peptidase |
| ? | NC_002947 | = 5201684 | 12 (0.670) | intergenic (‑122/‑58) | PP_4582/PP_4583 | membrane protein/putative Peptidase | |||||
| * | ? | NC_002947 | = 5382480 | 17 (0.680) | 3 (0.160) | 3/194 | 2.5 | 20.3% | intergenic (+52/+81) | smpB/pdhR | SsrA‑binding protein/DNA‑binding transcriptional regulator LldR |
| ? | NC_002947 | = 5382508 | 11 (0.600) | intergenic (+80/+53) | smpB/pdhR | SsrA‑binding protein/DNA‑binding transcriptional regulator LldR | |||||
| * | ? | NC_002947 | 5415552 = | 16 (0.640) | 4 (0.170) | 4/256 | 2.8 | 21.9% | coding (273/1392 nt) | gabP‑V | gamma‑aminobutyrate permease |
| ? | NC_002947 | 5415582 = | 13 (0.540) | coding (243/1392 nt) | gabP‑V | gamma‑aminobutyrate permease | |||||
| * | ? | NC_002947 | = 5454649 | NA (NA) | 8 (0.330) | 4/254 | 2.7 | NA | coding (1260/1329 nt) | PP_4791 | transposase |
| ? | NC_002947 | 5545214 = | NA (NA) | intergenic (‑306/+571) | rpsF/rlmB | 30S ribosomal protein S6/23S rRNA (guanosine(2251)‑2'‑O)‑methyltransferase RlmB | |||||
| * | ? | NC_002947 | = 5537105 | 18 (0.720) | 4 (0.200) | 4/210 | 2.3 | 20.3% | intergenic (+34/+69) | nadE/PP_4870 | NH(3)‑dependent NAD(+) synthetase/azurin |
| ? | NC_002947 | = 5537127 | 17 (0.860) | intergenic (+56/+47) | nadE/PP_4870 | NH(3)‑dependent NAD(+) synthetase/azurin | |||||
| * | ? | NC_002947 | 5743392 = | 23 (0.930) | 7 (0.310) | 7/238 | 1.7 | 24.2% | intergenic (‑169/+78) | fbp/glgP | class 1 fructose‑1,6‑bisphosphatase/glycogen phosphorylase |
| ? | NC_002947 | 5743446 = | 23 (1.030) | intergenic (‑223/+24) | fbp/glgP | class 1 fructose‑1,6‑bisphosphatase/glycogen phosphorylase | |||||
| * | ? | NC_002947 | 5759460 = | 30 (1.210) | 4 (0.210) | 4/200 | 2.2 | 20.1% | intergenic (+13/+143) | trmL/secB | tRNA (cytosine(34)‑2'‑O)‑methyltransferase TrmL/protein‑export protein SecB |
| ? | NC_002947 | 5759552 = | 9 (0.480) | intergenic (+105/+51) | trmL/secB | tRNA (cytosine(34)‑2'‑O)‑methyltransferase TrmL/protein‑export protein SecB | |||||
| * | ? | NC_002947 | 5914213 = | 27 (1.090) | 5 (0.260) | 5/208 | 2.0 | 22.1% | intergenic (+49/+104) | spuI/argA | glutamylpolyamine synthetase/amino acid N‑acetyltransferase |
| ? | NC_002947 | 5914309 = | 14 (0.720) | intergenic (+145/+8) | spuI/argA | glutamylpolyamine synthetase/amino acid N‑acetyltransferase | |||||
| * | ? | NC_002947 | 6006595 = | 30 (1.210) | 11 (0.610) | 11/192 | 0.7 | 47.0% | intergenic (+7/+92) | ydcJ/PP_5261 | metalloprotein/LysR family transcriptional regulator |
| ? | NC_002947 | 6006679 = | 3 (0.170) | intergenic (+91/+8) | ydcJ/PP_5261 | metalloprotein/LysR family transcriptional regulator | |||||