mutation predictions | marginal predictions | summary statistics | genome diff | command line log
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breseq version 0.35.4 revision f352f80f4bc9
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Marginal read alignment evidence (highest frequency 20 of 36 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_002947_CJ‑RC | 1,712,075 | 0 | G | T | 57.1% | ‑6.5 / 14.0 | 15 | intergenic (+66/‑192) | ppc/adk | phosphoenolpyruvate carboxylase/adenylate kinase |
| * | NC_002947_CJ‑RC | 3,447,291 | 0 | T | G | 54.8% | ‑2.7 / 25.7 | 33 | A19A (GCT→GCG) | PP_5556 | bacteriophage lysis protein |
| * | NC_002947_CJ‑RC | 1,327,121 | 0 | C | T | 54.7% | 34.1 / 220.5 | 159 | intergenic (+97/‑196) | PP_16SE/PP_23SE | 16S ribosomal RNA/23S ribosomal RNA |
| * | NC_002947_CJ‑RC | 697,094 | 0 | A | G | 54.2% | ‑2.0 / 24.2 | 27 | intergenic (+21/‑730) | mmsA‑I/PP_16SD | methylmalonate‑semialdehyde dehydrogenase/16S ribosomal RNA |
| * | NC_002947_CJ‑RC | 1,712,090 | 0 | G | C | 53.3% | 5.1 / 15.0 | 15 | intergenic (+81/‑177) | ppc/adk | phosphoenolpyruvate carboxylase/adenylate kinase |
| * | NC_002947_CJ‑RC | 195,634 | 0 | C | T | 49.6% | 19.9 / 181.1 | 125 | T380T (ACC→ACT) | PP_0168 | putative surface adhesion protein |
| * | NC_002947_CJ‑RC | 699,722 | 0 | A | G | 48.0% | 23.5 / 175.8 | 123 | intergenic (+115/‑129) | PP_t06/PP_23SD | tRNA‑Ala/23S ribosomal RNA |
| * | NC_002947_CJ‑RC | 4,348,812 | 0 | A | G | 44.5% | 75.5 / 160.4 | 119 | intergenic (‑70/+404) | PP_3820/galU | group II intron‑encoding maturase/UTP‑glucose‑1‑phosphate uridylyltransferase |
| * | NC_002947_CJ‑RC | 5,164,232 | 0 | C | G | 42.9% | 44.0 / 13.8 | 42 | intergenic (+52/+149) | PP_4544/PP_4545 | hypothetical protein/beta‑ketodecanoyl‑ACP synthase |
| * | NC_002947_CJ‑RC | 697,114 | 0 | T | G | 38.9% | 41.4 / 11.7 | 37 | intergenic (+41/‑710) | mmsA‑I/PP_16SD | methylmalonate‑semialdehyde dehydrogenase/16S ribosomal RNA |
| * | NC_002947_CJ‑RC | 923,653 | 0 | C | A | 34.7% | 102.2 / 11.7 | 49 | D514Y (GAT→TAT) | PP_0804 | protein secretion ABC transporter permease/ATP‑binding protein |
| * | NC_002947_CJ‑RC | 5,923,026 | 0 | A | C | 34.2% | 57.6 / 12.3 | 42 | K266T (AAG→ACG) | PP_5190 | type II secretion system protein |
| * | NC_002947_CJ‑RC | 1,703,248 | 0 | A | G | 33.3% | 21.5 / 18.4 | 24 | intergenic (+97/‑70) | lysS/PP_1497 | lysine‑‑tRNA ligase/TetR family transcriptional regulator |
| * | NC_002947_CJ‑RC | 5,164,209 | 0 | C | G | 33.3% | 87.7 / 14.0 | 51 | intergenic (+29/+172) | PP_4544/PP_4545 | hypothetical protein/beta‑ketodecanoyl‑ACP synthase |
| * | NC_002947_CJ‑RC | 5,164,207 | 0 | A | C | 32.6% | 69.9 / 12.9 | 52 | intergenic (+27/+174) | PP_4544/PP_4545 | hypothetical protein/beta‑ketodecanoyl‑ACP synthase |
| * | NC_002947_CJ‑RC | 1,703,250 | 0 | G | C | 32.0% | 28.8 / 24.3 | 25 | intergenic (+99/‑68) | lysS/PP_1497 | lysine‑‑tRNA ligase/TetR family transcriptional regulator |
| * | NC_002947_CJ‑RC | 1,703,252 | 0 | C | T | 32.0% | 27.2 / 17.4 | 25 | intergenic (+101/‑66) | lysS/PP_1497 | lysine‑‑tRNA ligase/TetR family transcriptional regulator |
| * | NC_002947_CJ‑RC | 1,013,234 | 0 | C | A | 31.8% | 37.5 / 15.0 | 22 | intergenic (+62/+69) | prfC/potF‑I | peptide chain release factor 3/putrescine‑binding protein |
| * | NC_002947_CJ‑RC | 2,282,770 | 0 | T | G | 30.0% | 23.8 / 11.9 | 20 | intergenic (‑162/+67) | PP_2010/PP_2011 | cytochrome b561/hypothetical protein |
| * | NC_002947_CJ‑RC | 2,120,838 | 0 | T | G | 28.2% | 67.1 / 11.7 | 39 | R663R (CGT→CGG) | PP_1885 | hypothetical protein |
| Marginal new junction evidence (lowest skew 10 of 39 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_002947_CJ‑RC | = 5558423 | 6 (0.080) | 21 (0.280) +GCC |
19/284 | 4.2 | 78.1% | intergenic (‑84/+87) | PP_4887/PP_4888 | hypothetical protein/methyl‑accepting chemotaxis transducer |
| ? | NC_002947_CJ‑RC | 5558424 = | 6 (0.080) | intergenic (‑85/+86) | PP_4887/PP_4888 | hypothetical protein/methyl‑accepting chemotaxis transducer | |||||
| * | ? | NC_002947_CJ‑RC | 4809877 = | 1 (0.010) | 16 (0.270) | 13/220 | 4.3 | 51.0% | intergenic (‑283/‑272) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947_CJ‑RC | = 5991750 | 30 (0.520) | intergenic (+229/‑317) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947_CJ‑RC | = 5684230 | 1 (0.010) | 14 (0.190) +CGGG |
12/282 | 6.0 | 93.5% | intergenic (‑133/+71) | PP_4986/PP_4987 | hemolysin III family channel protein/putative Chemotaxis protein |
| ? | NC_002947_CJ‑RC | 5684231 = | 1 (0.010) | intergenic (‑134/+70) | PP_4986/PP_4987 | hemolysin III family channel protein/putative Chemotaxis protein | |||||
| * | ? | NC_002947_CJ‑RC | = 4809882 | 3 (0.040) | 13 (0.180) | 9/266 | 6.8 | 30.0% | intergenic (‑288/‑267) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947_CJ‑RC | 5991580 = | 58 (0.820) | intergenic (+59/‑487) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947_CJ‑RC | = 1780066 | 16 (0.210) | 9 (0.120) | 9/276 | 7.0 | 33.2% | intergenic (+25/+81) | PP_1587/dapC | NhaP‑type Na+(K+)/H+ antiporter/N‑succinyl‑L,L‑diaminopimelate aminotransferase |
| ? | NC_002947_CJ‑RC | 1780129 = | 21 (0.290) | intergenic (+88/+18) | PP_1587/dapC | NhaP‑type Na+(K+)/H+ antiporter/N‑succinyl‑L,L‑diaminopimelate aminotransferase | |||||
| * | ? | NC_002947_CJ‑RC | 2099960 = | 18 (0.230) | 5 (0.080) | 5/244 | 8.1 | 23.7% | intergenic (‑71/‑134) | PP_1875/PP_1876 | two‑component system sensor histidine kinase/response regulator/AAA family ATP/GTP‑binding protein |
| ? | NC_002947_CJ‑RC | 2100055 = | 17 (0.260) | intergenic (‑166/‑39) | PP_1875/PP_1876 | two‑component system sensor histidine kinase/response regulator/AAA family ATP/GTP‑binding protein | |||||
| * | ? | NC_002947_CJ‑RC | = 1799873 | 31 (0.400) | 8 (0.120) | 5/244 | 8.1 | 20.0% | intergenic (+43/‑144) | rnhB/dnaEA | ribonuclease HII/DNA polymerase III subunit alpha |
| ? | NC_002947_CJ‑RC | = 1799915 | 38 (0.590) | intergenic (+85/‑102) | rnhB/dnaEA | ribonuclease HII/DNA polymerase III subunit alpha | |||||
| * | ? | NC_002947_CJ‑RC | 5164273 = | 34 (0.440) | 4 (0.060) | 4/238 | 8.5 | 11.0% | intergenic (+93/+108) | PP_4544/PP_4545 | hypothetical protein/beta‑ketodecanoyl‑ACP synthase |
| ? | NC_002947_CJ‑RC | 5164357 = | 37 (0.590) | intergenic (+177/+24) | PP_4544/PP_4545 | hypothetical protein/beta‑ketodecanoyl‑ACP synthase | |||||
| * | ? | NC_002947_CJ‑RC | 4891272 = | 35 (0.460) | 4 (0.060) | 4/236 | 8.5 | 11.9% | intergenic (+15/‑138) | hyi/glxR | hydroxypyruvate isomerase/2‑hydroxy‑3‑oxopropionate reductase |
| ? | NC_002947_CJ‑RC | 4891363 = | 31 (0.500) | intergenic (+106/‑47) | hyi/glxR | hydroxypyruvate isomerase/2‑hydroxy‑3‑oxopropionate reductase | |||||
| * | ? | NC_002947_CJ‑RC | 4647664 = | 29 (0.380) | 3 (0.050) | 3/212 | 8.5 | 11.5% | intergenic (+10/+121) | fusB/PP_4112 | elongation factor G 2/sulfate transporter |
| ? | NC_002947_CJ‑RC | 4647772 = | 25 (0.450) | intergenic (+118/+13) | fusB/PP_4112 | elongation factor G 2/sulfate transporter | |||||