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 | annotation | gene | description |
| JC | 1,851,823 | (TGCG)2→3 | coding (867/2241 nt) | relA → | ATP:GTP 3'‑pyrophosphotransferase |
| RA | 4,741,273 | +C | intergenic (+464/+288) | gltA → / ← yeiW | citrate synthase/putative oxidoreductase |
| RA | 4,741,275 | A→G | intergenic (+466/+286) | gltA → / ← yeiW | citrate synthase/putative oxidoreductase |
| RA | 4,741,277 | C→T | intergenic (+468/+284) | gltA → / ← yeiW | citrate synthase/putative oxidoreductase |
| RA | 4,741,280 | C→T | intergenic (+471/+281) | 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 |
| RA | 4,965,027 | C→A | E126* (GAA→TAA) | fleQ ← | transcriptional regulator FleQ |
| RA | 5,656,850 | C→A | G299V (GGT→GTT) | tktA ← | transketolase A |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_002947 | 171391–173337 | 173337 | 1–1947 | 2 [1] | [1] 2 | [PP_16SA]–[PP_23SA] | [PP_16SA],[PP_23SA] |
| * | * | ÷ | NC_002947 | 176681–181683 | 181683 | 1–5003 | 2 [1] | [1] 2 | PP_16SB–[PP_r01] | PP_16SB,PP_23SB,[PP_r01] |
| * | * | ÷ | NC_002947 | 2016757 | 2016800 | 44 | 3 [0] | [1] 2 | PP_1795/PP_1797 | hypothetical protein/HlyD family secretion protein |
| * | * | ÷ | NC_002947 | 2185558 | 2185606 | 49 | 2 [1] | [0] 2 | PP_1936 | membrane protein |
| * | * | ÷ | NC_002947 | 2594791 | 2594828 | 38 | 2 [1] | [1] 2 | PP_2272 | hypothetical protein |
| * | * | ÷ | NC_002947 | 3053556 | 3053603 | 48 | 2 [1] | [1] 2 | agmR | glycerol metabolism activator |
| * | * | ÷ | NC_002947 | 4808205 | 4808241 | 37 | 10 [0] | [1] 2 | 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 | = 174906 | NA (NA) | 3 (0.180) | 3/268 | 2.0 | NA | noncoding (1704/2902 nt) | PP_23SA | 23S ribosomal RNA |
| ? | NC_002947 | = 174936 | NA (NA) | noncoding (1734/2902 nt) | PP_23SA | 23S ribosomal RNA | |||||
| * | ? | NC_002947 | = 316022 | 17 (1.000) | 5 (0.310) | 5/268 | 1.4 | 30.9% | intergenic (+34/+49) | cysQ/PP_0262 | 3'(2'),5'‑bisphosphate nucleotidase CysQ/hypothetical protein |
| ? | NC_002947 | 336297 = | 6 (0.370) | intergenic (+142/+251) | PP_0278/PP_0279 | hypothetical protein/hypothetical protein | |||||
| * | ? | NC_002947 | = 358087 | 1 (0.060) | 4 (0.310) | 4/212 | 1.3 | 82.0% | intergenic (+52/‑78) | tdcG‑I/PP_5441 | L‑serine dehydratase/hypothetical protein |
| ? | NC_002947 | = 358099 | 1 (0.080) | intergenic (+64/‑66) | tdcG‑I/PP_5441 | L‑serine dehydratase/hypothetical protein | |||||
| * | ? | NC_002947 | = 652785 | 24 (1.420) | 7 (0.480) | 6/238 | 1.0 | 40.5% | coding (1961/1962 nt) | ctpL | methyl‑accepting chemotaxis protein CtpL |
| ? | NC_002947 | = 4808204 | 0 (0.000) | intergenic (‑268/‑287) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 | |||||
| * | ? | NC_002947 | 741473 = | NA (NA) | 4 (0.240) | 4/270 | 1.7 | 22.7% | intergenic (+70/‑430) | PP_t12/PP_0635 | tRNA‑Thr/group II intron‑encoding maturase |
| ? | NC_002947 | 2069206 = | 14 (0.830) | intergenic (+10/‑464) | PP_t19/PP_1846 | tRNA‑Ser/group II intron‑encoding maturase | |||||
| * | ? | NC_002947 | 1037774 = | 9 (0.530) | 4 (0.280) | 3/232 | 1.7 | 37.2% | intergenic (+16/+100) | PP_0896/PP_0897 | carbon‑nitrogen hydrolase family protein/class 1 fumarate hydratase |
| ? | NC_002947 | 1037852 = | 6 (0.420) | intergenic (+94/+22) | PP_0896/PP_0897 | carbon‑nitrogen hydrolase family protein/class 1 fumarate hydratase | |||||
| * | ? | NC_002947 | 1296580 = | NA (NA) | 5 (0.320) | 5/260 | 1.4 | NA | intergenic (‑327/‑239) | nhaA‑I/PP_1133 | Na(+)/H(+) antiporter NhaA/transposase |
| ? | NC_002947 | 1296616 = | NA (NA) | intergenic (‑363/‑203) | nhaA‑I/PP_1133 | Na(+)/H(+) antiporter NhaA/transposase | |||||
| * | ? | NC_002947 | 1306459 = | 11 (0.650) | 3 (0.190) | 3/260 | 1.9 | 21.2% | intergenic (‑137/+49) | livH/livK | branched‑chain amino acid ABC transporter permease/branched‑chain amino acids ABC transporter substrate‑binding protein |
| ? | NC_002947 | 1306483 = | 12 (0.760) | intergenic (‑161/+25) | livH/livK | branched‑chain amino acid ABC transporter permease/branched‑chain amino acids ABC transporter substrate‑binding protein | |||||
| * | ? | NC_002947 | 1436017 = | 14 (0.830) | 4 (0.240) | 3/278 | 2.0 | 21.6% | intergenic (‑47/+106) | PP_1256/PP_1257 | alpha‑ketoglutarate semialdehyde dehydrogenase/1‑pyrroline‑4‑hydroxy‑2‑carboxylate deaminase |
| ? | NC_002947 | 1436110 = | 15 (0.890) | intergenic (‑140/+13) | PP_1256/PP_1257 | alpha‑ketoglutarate semialdehyde dehydrogenase/1‑pyrroline‑4‑hydroxy‑2‑carboxylate deaminase | |||||
| * | ? | NC_002947 | 1443111 = | 9 (0.530) | 4 (0.290) | 4/228 | 1.4 | 46.0% | intergenic (‑42/+134) | ghrB/PP_1262 | 2‑ketoaldonate reductase/hydroxypyruvate/glyoxylate reductase/LysR family transcriptional regulator |
| ? | NC_002947 | 1443179 = | 2 (0.140) | intergenic (‑110/+66) | ghrB/PP_1262 | 2‑ketoaldonate reductase/hydroxypyruvate/glyoxylate reductase/LysR family transcriptional regulator | |||||
| * | ? | NC_002947 | 1499443 = | 9 (0.530) | 4 (0.280) | 4/232 | 1.4 | 41.0% | intergenic (+13/‑153) | trpS/zapE | tryptophan‑‑tRNA ligase/nucleoside triphosphate hydrolase domain‑containing protein |
| ? | NC_002947 | 1499526 = | 4 (0.280) | intergenic (+96/‑70) | trpS/zapE | tryptophan‑‑tRNA ligase/nucleoside triphosphate hydrolase domain‑containing protein | |||||
| * | ? | NC_002947 | 1690813 = | 15 (0.890) | 4 (0.240) | 4/274 | 1.7 | 21.8% | coding (60/1146 nt) | ydcS | polyamine ABC transporter, periplasmic polyamine‑binding protein |
| ? | NC_002947 | 1690835 = | 14 (0.840) | coding (38/1146 nt) | ydcS | polyamine ABC transporter, periplasmic polyamine‑binding protein | |||||
| * | ? | NC_002947 | = 1780127 | 7 (0.410) | 3 (0.210) | 3/240 | 1.8 | 35.2% | intergenic (+44/+62) | PP_1587/dapC | NhaP‑type Na+(K+)/H+ antiporter/N‑succinyl‑L,L‑diaminopimelate aminotransferase |
| ? | NC_002947 | = 1780151 | 5 (0.340) | intergenic (+68/+38) | PP_1587/dapC | NhaP‑type Na+(K+)/H+ antiporter/N‑succinyl‑L,L‑diaminopimelate aminotransferase | |||||
| * | ? | NC_002947 | 1967181 = | 5 (0.300) | 4 (0.240) | 4/270 | 1.7 | 42.4% | intergenic (+8/+111) | PP_1762/yciK | hypothetical protein/putative oxidoreductase |
| ? | NC_002947 | 1967291 = | 6 (0.370) | intergenic (+118/+1) | PP_1762/yciK | hypothetical protein/putative oxidoreductase | |||||
| * | ? | NC_002947 | = 2057866 | 14 (0.830) | 5 (0.360) | 5/230 | 1.2 | 35.0% | intergenic (+39/+89) | PP_1832/PP_1833 | oxidase/hypothetical protein |
| ? | NC_002947 | = 2057906 | 7 (0.500) | intergenic (+79/+49) | PP_1832/PP_1833 | oxidase/hypothetical protein | |||||
| * | ? | NC_002947 | 2241317 = | 4 (0.240) | 4 (0.270) | 4/244 | 1.5 | 59.2% | intergenic (+21/‑260) | gltX/PP_t25 | glutamate‑‑tRNA ligase/tRNA‑Ala |
| ? | NC_002947 | 2241387 = | 2 (0.130) | intergenic (+91/‑190) | gltX/PP_t25 | glutamate‑‑tRNA ligase/tRNA‑Ala | |||||
| * | ? | NC_002947 | = 2253844 | 10 (0.590) | 3 (0.180) | 3/270 | 2.0 | 25.3% | coding (120/1083 nt) | leuB | 3‑isopropylmalate dehydrogenase |
| ? | NC_002947 | = 2253880 | 8 (0.490) | coding (156/1083 nt) | leuB | 3‑isopropylmalate dehydrogenase | |||||
| * | ? | NC_002947 | = 2472183 | 3 (0.180) | 4 (0.280) +21 bp |
4/236 | 1.5 | 22.8% | intergenic (+44/+105) | PP_2166/PP_2167 | anti‑anti‑sigma factor/PhoD‑like phosphatase |
| ? | NC_002947 | = 5574160 | 29 (1.710) | intergenic (+161/+144) | rsgA/motB | ribosome biogenesis GTPase RsgA/flagellar motor rotation protein | |||||
| * | ? | NC_002947 | 3947957 = | 7 (0.410) | 4 (0.300) | 4/222 | 1.4 | 45.5% | coding (136/1797 nt) | PP_3483 | type II secretion system protein |
| ? | NC_002947 | 3948042 = | 4 (0.300) | coding (51/1797 nt) | PP_3483 | type II secretion system protein | |||||
| * | ? | NC_002947 | 4222784 = | 12 (0.710) | 4 (0.240) | 4/270 | 1.7 | 25.3% | coding (115/204 nt) | PP_3701 | hypothetical protein |
| ? | NC_002947 | 4222804 = | 12 (0.730) | coding (95/204 nt) | PP_3701 | hypothetical protein | |||||
| * | ? | NC_002947 | 4348362 = | NA (NA) | 4 (0.250) | 4/266 | 1.6 | NA | coding (318/1422 nt) | PP_3820 | group II intron‑encoding maturase |
| ? | NC_002947 | 4392757 = | NA (NA) | coding (302/1422 nt) | PP_3868 | group II intron‑encoding maturase | |||||
| * | ? | NC_002947 | 4444087 = | 13 (0.770) | 4 (0.240) | 4/272 | 1.7 | 25.2% | intergenic (‑62/+147) | nicT/nicF | metabolite transport protein NicT/maleamate amidohydrolase |
| ? | NC_002947 | 4444116 = | 11 (0.660) | intergenic (‑91/+118) | nicT/nicF | metabolite transport protein NicT/maleamate amidohydrolase | |||||
| * | ? | NC_002947 | = 4896443 | 12 (0.710) | 4 (0.280) | 4/236 | 1.5 | 37.8% | intergenic (+31/‑177) | PP_4304/sbp‑I | VIC family cation transporter/sulfate ABC transporter substrate‑binding protein |
| ? | NC_002947 | = 4896490 | 3 (0.210) | intergenic (+78/‑130) | PP_4304/sbp‑I | VIC family cation transporter/sulfate ABC transporter substrate‑binding protein | |||||
| * | ? | NC_002947 | 5125135 = | 8 (0.470) | 3 (0.220) | 3/226 | 1.7 | 25.5% | intergenic (+61/‑121) | PP_4511/PP_4512 | AraC family transcriptional regulator/DMT superfamily permease |
| ? | NC_002947 | 5125214 = | 11 (0.800) | intergenic (+140/‑42) | PP_4511/PP_4512 | AraC family transcriptional regulator/DMT superfamily permease | |||||
| * | ? | NC_002947 | 5162618 = | 10 (0.590) | 6 (0.440) | 3/226 | 1.7 | 45.9% | intergenic (+93/+108) | PP_4544/PP_4545 | hypothetical protein/beta‑ketodecanoyl‑ACP synthase |
| ? | NC_002947 | 5162702 = | 6 (0.440) | intergenic (+177/+24) | PP_4544/PP_4545 | hypothetical protein/beta‑ketodecanoyl‑ACP synthase | |||||
| * | ? | NC_002947 | = 5201663 | 6 (0.350) | 4 (0.320) | 3/204 | 1.5 | 41.2% | intergenic (‑101/‑79) | PP_4582/PP_4583 | membrane protein/putative Peptidase |
| ? | NC_002947 | = 5201684 | 7 (0.560) | intergenic (‑122/‑58) | PP_4582/PP_4583 | membrane protein/putative Peptidase | |||||
| * | ? | NC_002947 | 5333243 = | 21 (1.240) | 6 (0.400) | 6/248 | 1.1 | 24.6% | intergenic (+27/‑216) | gluQ/PP_5704 | glutamyl‑Q tRNA(Asp) synthetase/hypothetical protein |
| ? | NC_002947 | 5333303 = | 18 (1.190) | intergenic (+87/‑156) | gluQ/PP_5704 | glutamyl‑Q tRNA(Asp) synthetase/hypothetical protein | |||||
| * | ? | NC_002947 | = 5594170 | 6 (0.350) | 3 (0.220) | 3/222 | 1.6 | 38.0% | intergenic (‑66/+79) | PP_4921/thiC | NCS1 family transporter/phosphomethylpyrimidine synthase |
| ? | NC_002947 | = 5594207 | 5 (0.370) | intergenic (‑103/+42) | PP_4921/thiC | NCS1 family transporter/phosphomethylpyrimidine synthase | |||||
| * | ? | NC_002947 | 5652989 = | 11 (0.650) | 3 (0.210) | 3/236 | 1.7 | 28.1% | intergenic (‑39/+122) | PP_4961/PP_4962 | lipoprotein/hypothetical protein |
| ? | NC_002947 | 5653045 = | 6 (0.420) | intergenic (‑95/+66) | PP_4961/PP_4962 | lipoprotein/hypothetical protein | |||||
| * | ? | NC_002947 | 5743392 = | 18 (1.060) | 4 (0.260) | 4/252 | 1.6 | 20.9% | intergenic (‑169/+78) | fbp/glgP | class 1 fructose‑1,6‑bisphosphatase/glycogen phosphorylase |
| ? | NC_002947 | 5743446 = | 14 (0.910) | intergenic (‑223/+24) | fbp/glgP | class 1 fructose‑1,6‑bisphosphatase/glycogen phosphorylase | |||||
| * | ? | NC_002947 | = 5759491 | 9 (0.530) | 4 (0.310) | 4/214 | 1.3 | 32.1% | intergenic (+44/+112) | trmL/secB | tRNA (cytosine(34)‑2'‑O)‑methyltransferase TrmL/protein‑export protein SecB |
| ? | NC_002947 | = 5759519 | 10 (0.770) | intergenic (+72/+84) | trmL/secB | tRNA (cytosine(34)‑2'‑O)‑methyltransferase TrmL/protein‑export protein SecB | |||||
| * | ? | NC_002947 | 5897799 = | 11 (0.650) | 4 (0.290) | 4/224 | 1.4 | 35.0% | intergenic (‑143/+91) | PP_5172/PP_5173 | hypothetical protein/RND family transporter |
| ? | NC_002947 | 5897875 = | 6 (0.440) | intergenic (‑219/+15) | PP_5172/PP_5173 | hypothetical protein/RND family transporter | |||||
| * | ? | NC_002947 | 6009165 = | 4 (0.240) | 4 (0.310) | 6/212 | 0.9 | 72.4% | intergenic (+6/+76) | norM/PP_5263 | multidrug resistance protein NorM/GGDEF domain‑containing protein |
| ? | NC_002947 | 6009242 = | 0 (0.000) | coding (1667/1668 nt) | PP_5263 | GGDEF domain‑containing protein | |||||
| * | ? | NC_002947 | 6032797 = | 11 (0.650) | 4 (0.240) | 4/270 | 1.7 | 23.8% | intergenic (+5/+131) | dppA‑IV/PP_5284 | dipeptide transport protein/hypothetical protein |
| ? | NC_002947 | 6032901 = | 15 (0.910) | intergenic (+109/+27) | dppA‑IV/PP_5284 | dipeptide transport protein/hypothetical protein | |||||
| * | ? | NC_002947 | = 6060500 | 9 (0.530) | 3 (0.200) | 3/250 | 1.8 | 21.4% | intergenic (+80/+101) | PP_5311/PP_5312 | signal transduction protein/hypothetical protein |
| ? | NC_002947 | = 6060559 | 14 (0.920) | intergenic (+139/+42) | PP_5311/PP_5312 | signal transduction protein/hypothetical protein | |||||
| * | ? | NC_002947 | = 6097786 | 9 (0.530) | 3 (0.190) | 3/258 | 1.9 | 22.8% | coding (844/963 nt) | PP_5348 | LysR family transcriptional regulator |
| ? | NC_002947 | = 6097801 | 12 (0.760) | coding (859/963 nt) | PP_5348 | LysR family transcriptional regulator | |||||