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 | 1,843,935 | G→A | L301F (CTC→TTC) | gacS ← | sensor protein GacS |
| RA | 1,851,914 | G→T | D320Y (GAC→TAC) | relA → | ATP:GTP 3'‑pyrophosphotransferase |
| RA | 4,741,273 | +C | intergenic (+464/+288) | gltA → / ← yeiW | citrate synthase/putative oxidoreductase |
| 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 | 171405–172965 | 176278–172969 | 5–4874 | 2 [1] | [1] 2 | [PP_16SA]–[PP_5SA] | [PP_16SA],PP_23SA,[PP_5SA] |
| * | * | ÷ | NC_002947 | 176676–178395 | 181678–178399 | 5–5003 | 2 [1] | [0] 2 | PP_16SB–[PP_r01] | PP_16SB,PP_23SB,[PP_r01] |
| * | * | ÷ | NC_002947 | 1131740 | 1131806 | 67 | 2 [1] | [0] 2 | PP_0992 | hypothetical protein |
| * | * | ÷ | NC_002947 | 1370992 | 1371011 | 20 | 2 [0] | [1] 2 | PP_1196 | hypothetical protein |
| * | * | ÷ | NC_002947 | 2167109 | 2167154 | 46 | 3 [1] | [1] 2 | PP_1921 | hypothetical protein |
| * | * | ÷ | NC_002947 | 3109048 | 3109133 | 86 | 2 [1] | [1] 2 | PP_2722 | hypothetical protein |
| * | * | ÷ | NC_002947 | 3160600 | 3160629 | 30 | 3 [1] | [1] 2 | PP_2775 | glycine betaine/L‑proline ABC transporter substrate‑binding protein |
| * | * | ÷ | NC_002947 | 3445437 | 3445467 | 31 | 2 [1] | [1] 2 | PP_3064 | tail protein |
| * | * | ÷ | NC_002947 | 3676183 | 3676215 | 33 | 2 [1] | [0] 2 | PP_5592 | hypothetical protein |
| * | * | ÷ | NC_002947 | 3740990 | 3741029 | 40 | 2 [1] | [1] 3 | [PP_3305] | [PP_3305] |
| * | * | ÷ | NC_002947 | 5414289 | 5414405 | 117 | 2 [1] | [1] 3 | PP_4755/gabP‑V | ferrichrome‑iron receptor/gamma‑aminobutyrate permease |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_002947 | 414338 = | 13 (0.760) | 3 (0.180) | 3/268 | 1.9 | 20.3% | coding (153/1050 nt) | waaF | ADP‑heptose:LPS heptosyltransferase II |
| ? | NC_002947 | 414374 = | 11 (0.660) | coding (189/1050 nt) | waaF | ADP‑heptose:LPS heptosyltransferase II | |||||
| * | ? | NC_002947 | 796307 = | 17 (0.990) | 4 (0.260) | 4/254 | 1.5 | 22.5% | intergenic (+7/‑156) | PP_0680/PP_0681 | ATP‑dependent protease‑like protein/hypothetical protein |
| ? | NC_002947 | 796350 = | 12 (0.770) | intergenic (+50/‑113) | PP_0680/PP_0681 | ATP‑dependent protease‑like protein/hypothetical protein | |||||
| * | ? | NC_002947 | 1037774 = | 21 (1.220) | 4 (0.280) | 3/232 | 1.7 | 20.8% | intergenic (+16/+100) | PP_0896/PP_0897 | carbon‑nitrogen hydrolase family protein/class 1 fumarate hydratase |
| ? | NC_002947 | 1037852 = | 13 (0.910) | intergenic (+94/+22) | PP_0896/PP_0897 | carbon‑nitrogen hydrolase family protein/class 1 fumarate hydratase | |||||
| * | ? | NC_002947 | = 1114899 | 14 (0.820) | 5 (0.360) | 5/228 | 1.1 | 28.2% | intergenic (‑88/+91) | rlmF/valS | ribosomal RNA large subunit methyltransferase F/valine‑‑tRNA ligase |
| ? | NC_002947 | = 1114925 | 14 (1.000) | intergenic (‑114/+65) | rlmF/valS | ribosomal RNA large subunit methyltransferase F/valine‑‑tRNA ligase | |||||
| * | ? | NC_002947 | 1436018 = | 16 (0.930) | 4 (0.240) | 4/266 | 1.6 | 22.0% | intergenic (‑48/+105) | PP_1256/PP_1257 | alpha‑ketoglutarate semialdehyde dehydrogenase/1‑pyrroline‑4‑hydroxy‑2‑carboxylate deaminase |
| ? | NC_002947 | 1436109 = | 13 (0.790) | intergenic (‑139/+14) | PP_1256/PP_1257 | alpha‑ketoglutarate semialdehyde dehydrogenase/1‑pyrroline‑4‑hydroxy‑2‑carboxylate deaminase | |||||
| * | ? | NC_002947 | 1621292 = | 13 (0.760) | 4 (0.250) | 4/258 | 1.6 | 24.2% | coding (164/1392 nt) | PP_1421 | sensor histidine kinase TctE |
| ? | NC_002947 | 1621329 = | 13 (0.820) | coding (201/1392 nt) | PP_1421 | sensor histidine kinase TctE | |||||
| * | ? | NC_002947 | 1731205 = | 13 (0.760) | 3 (0.220) | 3/222 | 1.6 | 28.1% | intergenic (‑76/+115) | dapE/PP_1526 | succinyl‑diaminopimelate desuccinylase/beta‑(1‑3)‑glucosyl transferase |
| ? | NC_002947 | 1731297 = | 5 (0.370) | intergenic (‑168/+23) | dapE/PP_1526 | succinyl‑diaminopimelate desuccinylase/beta‑(1‑3)‑glucosyl transferase | |||||
| * | ? | NC_002947 | 1967188 = | 3 (0.170) | 7 (0.540) | 7/212 | 0.7 | 86.0% | intergenic (+15/+104) | PP_1762/yciK | hypothetical protein/putative oxidoreductase |
| ? | NC_002947 | 1967284 = | 0 (0.000) | intergenic (+111/+8) | PP_1762/yciK | hypothetical protein/putative oxidoreductase | |||||
| * | ? | NC_002947 | = 1967220 | 3 (0.170) | 7 (0.540) | 6/212 | 0.9 | 86.0% | intergenic (+47/+72) | PP_1762/yciK | hypothetical protein/putative oxidoreductase |
| ? | NC_002947 | = 1967250 | 0 (0.000) | intergenic (+77/+42) | PP_1762/yciK | hypothetical protein/putative oxidoreductase | |||||
| * | ? | NC_002947 | = 1970789 | 14 (0.820) | 6 (0.370) | 4/266 | 1.6 | 30.5% | intergenic (+40/‑226) | mtnA/PP_mr25 | methylthioribose‑1‑phosphate isomerase/gyrA regulatory region |
| ? | NC_002947 | = 1970837 | 14 (0.850) | intergenic (+88/‑178) | mtnA/PP_mr25 | methylthioribose‑1‑phosphate isomerase/gyrA regulatory region | |||||
| * | ? | NC_002947 | = 2048853 | 12 (0.700) | 4 (0.270) | 4/244 | 1.5 | 21.9% | intergenic (+49/+90) | PP_1821/PP_1822 | glutathione S‑transferase family protein/hypothetical protein |
| ? | NC_002947 | = 2048910 | 18 (1.200) | intergenic (+106/+33) | PP_1821/PP_1822 | glutathione S‑transferase family protein/hypothetical protein | |||||
| * | ? | NC_002947 | = 2085562 | 12 (0.700) | 6 (0.370) | 4/262 | 1.6 | 42.4% | intergenic (+228/‑367) | PP_1864/PP_1865 | hypothetical protein/transposase |
| ? | NC_002947 | = 2087716 | 5 (0.310) | intergenic (+486/+432) | PP_1865/aroH | transposase/3‑deoxy‑7‑phosphoheptulonate synthase | |||||
| * | ? | NC_002947 | 2301496 = | 0 (0.000) | 17 (1.010) | 12/272 | 0.5 | 100% | intergenic (‑97/‑234) | sbcD/PP_5497 | exonuclease subunit SbcD/rhs repeat‑associated core domain‑containing protein |
| ? | NC_002947 | 2925472 = | NA (NA) | intergenic (‑177/+388) | PP_2563/PP_2564 | antibiotic biosynthesis protein/quercetin 2,3‑dioxygenase | |||||
| * | ? | NC_002947 | = 2301497 | 0 (0.000) | 13 (0.770) | 13/274 | 0.4 | 100% | intergenic (‑98/‑233) | sbcD/PP_5497 | exonuclease subunit SbcD/rhs repeat‑associated core domain‑containing protein |
| ? | NC_002947 | 5545369 = | NA (NA) | intergenic (‑461/+416) | rpsF/rlmB | 30S ribosomal protein S6/23S rRNA (guanosine(2251)‑2'‑O)‑methyltransferase RlmB | |||||
| * | ? | NC_002947 | 2489400 = | 10 (0.580) | 4 (0.240) | 4/268 | 1.6 | 28.9% | coding (354/1578 nt) | PP_2184 | formate dehydrogenase subunit beta |
| ? | NC_002947 | 2489439 = | 10 (0.600) | coding (393/1578 nt) | PP_2184 | formate dehydrogenase subunit beta | |||||
| * | ? | NC_002947 | 2574385 = | 15 (0.870) | 5 (0.300) | 4/266 | 1.6 | 26.1% | coding (1098/1566 nt) | PP_2257 | aerotaxis receptor |
| ? | NC_002947 | 2574435 = | 14 (0.850) | coding (1148/1566 nt) | PP_2257 | aerotaxis receptor | |||||
| * | ? | NC_002947 | = 3108920 | 12 (0.700) | 3 (0.180) | 3/266 | 1.9 | 21.1% | coding (278/465 nt) | PP_2722 | hypothetical protein |
| ? | NC_002947 | = 3108938 | 11 (0.670) | coding (260/465 nt) | PP_2722 | hypothetical protein | |||||
| * | ? | NC_002947 | 3387807 = | 16 (0.930) | 5 (0.310) | 5/262 | 1.3 | 23.2% | coding (545/795 nt) | PP_2989 | short‑chain dehydrogenase/reductase family oxidoreductase |
| ? | NC_002947 | 3387849 = | 18 (1.110) | coding (587/795 nt) | PP_2989 | short‑chain dehydrogenase/reductase family oxidoreductase | |||||
| * | ? | NC_002947 | = 3522813 | 12 (0.700) | 4 (0.240) | 4/272 | 1.6 | 32.3% | intergenic (+557/‑140) | PP_5584/PP_3113 | hypothetical protein/transposase |
| ? | NC_002947 | = 3522862 | 5 (0.300) | intergenic (+606/‑91) | PP_5584/PP_3113 | hypothetical protein/transposase | |||||
| * | ? | NC_002947 | 3974772 = | 10 (0.580) | 3 (0.180) | 3/268 | 1.9 | 23.4% | intergenic (‑256/‑85) | PP_3503/PP_3504 | sigma‑54 dependent transcriptional regulator/hypothetical protein |
| ? | NC_002947 | 3974818 = | 10 (0.600) | intergenic (‑302/‑39) | PP_3503/PP_3504 | sigma‑54 dependent transcriptional regulator/hypothetical protein | |||||
| * | ? | NC_002947 | 4586063 = | 18 (1.050) | 3 (0.240) | 3/202 | 1.5 | 26.0% | intergenic (+102/+115) | PP_4061/PP_4063 | hypothetical protein/long‑chain fatty acid‑‑CoA ligase |
| ? | NC_002947 | 4586167 = | 4 (0.320) | intergenic (+206/+11) | PP_4061/PP_4063 | hypothetical protein/long‑chain fatty acid‑‑CoA ligase | |||||
| * | ? | NC_002947 | = 4808224 | 3 (0.170) | 6 (0.410) | 4/238 | 1.4 | 39.3% | intergenic (‑288/‑267) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947 | 4945248 = | 16 (1.090) | intergenic (+563/+235) | PP_5673/flhB | D‑alanine‑‑D‑alanine ligase/flagellin export apparatus substrate specificity protein | |||||
| * | ? | NC_002947 | 4893598 = | 9 (0.520) | 4 (0.290) | 4/224 | 1.3 | 31.7% | intergenic (+28/‑180) | pyk/PP_4302 | pyruvate kinase/urea transporter |
| ? | NC_002947 | 4893677 = | 10 (0.720) | intergenic (+107/‑101) | pyk/PP_4302 | pyruvate kinase/urea transporter | |||||
| * | ? | NC_002947 | = 4893624 | 8 (0.470) | 3 (0.220) | 3/224 | 1.6 | 26.7% | intergenic (+54/‑154) | pyk/PP_4302 | pyruvate kinase/urea transporter |
| ? | NC_002947 | = 4893649 | 10 (0.720) | intergenic (+79/‑129) | pyk/PP_4302 | pyruvate kinase/urea transporter | |||||
| * | ? | NC_002947 | = 4896443 | 16 (0.930) | 9 (0.620) | 6/236 | 1.0 | 40.4% | intergenic (+31/‑177) | PP_4304/sbp‑I | VIC family cation transporter/sulfate ABC transporter substrate‑binding protein |
| ? | NC_002947 | = 4896490 | 13 (0.890) | intergenic (+78/‑130) | PP_4304/sbp‑I | VIC family cation transporter/sulfate ABC transporter substrate‑binding protein | |||||
| * | ? | NC_002947 | = 5033278 | 2 (0.120) | 5 (0.300) | 5/266 | 1.4 | 37.2% | intergenic (+395/‑15) | PP_4435/PP_4437 | hypothetical protein/transposase |
| ? | NC_002947 | 6155309 = | 15 (0.910) | intergenic (‑63/+143) | PP_5398/PP_5399 | transposase/hypothetical protein | |||||
| * | ? | NC_002947 | = 5190394 | 9 (0.520) | 3 (0.190) | 3/258 | 1.8 | 28.1% | intergenic (‑81/+93) | PP_4570/cysK | hypothetical protein/cysteine synthase A |
| ? | NC_002947 | = 5190411 | 7 (0.440) | intergenic (‑98/+76) | PP_4570/cysK | hypothetical protein/cysteine synthase A | |||||
| * | ? | NC_002947 | = 5201663 | 8 (0.470) | 6 (0.480) | 6/204 | 0.8 | 52.5% | intergenic (‑101/‑79) | PP_4582/PP_4583 | membrane protein/putative Peptidase |
| ? | NC_002947 | = 5201684 | 5 (0.400) | intergenic (‑122/‑58) | PP_4582/PP_4583 | membrane protein/putative Peptidase | |||||
| * | ? | NC_002947 | 5288442 = | 11 (0.640) | 4 (0.300) | 4/218 | 1.3 | 37.0% | intergenic (‑75/+109) | PP_4660/mdaB | LysR family transcriptional regulator/drug activity modulator B |
| ? | NC_002947 | 5288536 = | 5 (0.370) | intergenic (‑169/+15) | PP_4660/mdaB | LysR family transcriptional regulator/drug activity modulator B | |||||
| * | ? | NC_002947 | = 5671689 | 14 (0.820) | 7 (0.490) | 4/230 | 1.4 | 35.4% | intergenic (+57/‑113) | PP_4978/PP_4979 | hypothetical protein/substrate‑binding protein |
| ? | NC_002947 | = 5671726 | 14 (0.990) | intergenic (+94/‑76) | PP_4978/PP_4979 | hypothetical protein/substrate‑binding protein | |||||
| * | ? | NC_002947 | 5750393 = | 15 (0.870) | 4 (0.240) | 4/268 | 1.6 | 20.8% | coding (1226/1455 nt) | thiI | tRNA sulfurtransferase |
| ? | NC_002947 | 5750415 = | 16 (0.970) | coding (1204/1455 nt) | thiI | tRNA sulfurtransferase | |||||
| * | ? | NC_002947 | 5914213 = | 20 (1.160) | 5 (0.370) | 5/222 | 1.1 | 28.6% | intergenic (+49/+104) | spuI/argA | glutamylpolyamine synthetase/amino acid N‑acetyltransferase |
| ? | NC_002947 | 5914309 = | 9 (0.660) | intergenic (+145/+8) | spuI/argA | glutamylpolyamine synthetase/amino acid N‑acetyltransferase | |||||
| * | ? | NC_002947 | 6027949 = | 23 (1.340) | 7 (0.480) | 6/236 | 1.0 | 30.1% | intergenic (‑37/+74) | PP_5277/kauB | MFS transporter/4‑guanidinobutyraldehyde dehydrogenase |
| ? | NC_002947 | 6028006 = | 13 (0.890) | intergenic (‑94/+17) | PP_5277/kauB | MFS transporter/4‑guanidinobutyraldehyde dehydrogenase | |||||