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 30 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 | 5,684,230 | 2 | . | G | 100.0% | 10.0 / NA | 5 | intergenic (‑133/+71) | PP_4986/PP_4987 | hemolysin III family channel protein/putative Chemotaxis protein |
| * | NC_002947_CJ‑RC | 5,684,230 | 3 | . | G | 100.0% | 10.1 / NA | 5 | intergenic (‑133/+71) | PP_4986/PP_4987 | hemolysin III family channel protein/putative Chemotaxis protein |
| * | NC_002947_CJ‑RC | 5,684,230 | 4 | . | G | 100.0% | 10.0 / NA | 5 | intergenic (‑133/+71) | PP_4986/PP_4987 | hemolysin III family channel protein/putative Chemotaxis protein |
| * | NC_002947_CJ‑RC | 4,348,812 | 0 | A | G | 58.3% | 15.7 / 131.6 | 115 | intergenic (‑70/+404) | PP_3820/galU | group II intron‑encoding maturase/UTP‑glucose‑1‑phosphate uridylyltransferase |
| * | NC_002947_CJ‑RC | 1,712,090 | 0 | G | C | 53.8% | 4.1 / 17.5 | 13 | intergenic (+81/‑177) | ppc/adk | phosphoenolpyruvate carboxylase/adenylate kinase |
| * | NC_002947_CJ‑RC | 2,099,945 | 0 | A | C | 53.3% | 3.5 / 14.4 | 16 | intergenic (‑56/‑149) | PP_1875/PP_1876 | two‑component system sensor histidine kinase/response regulator/AAA family ATP/GTP‑binding protein |
| * | NC_002947_CJ‑RC | 4,158,471 | 0 | A | C | 51.7% | ‑3.7 / 19.3 | 29 | S161R (AGC→CGC) | PP_3661 | membrane protein |
| * | NC_002947_CJ‑RC | 1,327,121 | 0 | C | T | 49.4% | 81.7 / 239.9 | 170 | intergenic (+97/‑196) | PP_16SE/PP_23SE | 16S ribosomal RNA/23S ribosomal RNA |
| * | NC_002947_CJ‑RC | 699,722 | 0 | A | G | 42.6% | 59.5 / 148.9 | 123 | intergenic (+115/‑129) | PP_t06/PP_23SD | tRNA‑Ala/23S ribosomal RNA |
| * | NC_002947_CJ‑RC | 5,987,264 | 0 | T | C | 36.8% | 12.9 / 15.8 | 20 | intergenic (+45/+44) | PP_5242/ycaC‑II | GAF domain‑containing sensor histidine kinase/putative hydrolase |
| * | NC_002947_CJ‑RC | 5,987,262 | 0 | G | A | 31.8% | 26.1 / 13.5 | 22 | intergenic (+43/+46) | PP_5242/ycaC‑II | GAF domain‑containing sensor histidine kinase/putative hydrolase |
| * | NC_002947_CJ‑RC | 5,987,251 | 0 | T | C | 30.4% | 27.1 / 15.1 | 23 | intergenic (+32/+57) | PP_5242/ycaC‑II | GAF domain‑containing sensor histidine kinase/putative hydrolase |
| * | NC_002947_CJ‑RC | 5,987,257 | 0 | G | A | 30.4% | 30.1 / 13.2 | 23 | intergenic (+38/+51) | PP_5242/ycaC‑II | GAF domain‑containing sensor histidine kinase/putative hydrolase |
| * | NC_002947_CJ‑RC | 5,987,259 | 0 | T | C | 30.4% | 27.7 / 15.1 | 23 | intergenic (+40/+49) | PP_5242/ycaC‑II | GAF domain‑containing sensor histidine kinase/putative hydrolase |
| * | NC_002947_CJ‑RC | 1,703,250 | 0 | G | C | 30.3% | 50.0 / 28.0 | 33 | intergenic (+99/‑68) | lysS/PP_1497 | lysine‑‑tRNA ligase/TetR family transcriptional regulator |
| * | NC_002947_CJ‑RC | 1,703,248 | 0 | A | G | 30.0% | 33.9 / 20.8 | 31 | intergenic (+97/‑70) | lysS/PP_1497 | lysine‑‑tRNA ligase/TetR family transcriptional regulator |
| * | NC_002947_CJ‑RC | 1,703,252 | 0 | C | T | 29.0% | 42.8 / 17.9 | 31 | intergenic (+101/‑66) | lysS/PP_1497 | lysine‑‑tRNA ligase/TetR family transcriptional regulator |
| * | NC_002947_CJ‑RC | 245,412 | 0 | A | G | 26.7% | 78.7 / 10.0 | 46 | S121P (TCC→CCC) | PP_0195 | hypothetical protein |
| * | NC_002947_CJ‑RC | 3,985,645 | 0 | A | C | 25.4% | 120.4 / 17.1 | 64 | intergenic (+74/‑79) | PP_3513/oplB | LysR family transcriptional regulator/5‑oxoprolinase B |
| * | NC_002947_CJ‑RC | 3,593,351 | 0 | C | A | 25.0% | 131.1 / 12.4 | 58 | F129L (TTC→TTA) | PP_3171 | hypothetical protein |
| Marginal new junction evidence (lowest skew 10 of 52 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_002947_CJ‑RC | 4809877 = | 8 (0.100) | 15 (0.250) | 13/220 | 5.3 | 34.9% | intergenic (‑283/‑272) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947_CJ‑RC | = 5991750 | 50 (0.840) | intergenic (+229/‑317) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947_CJ‑RC | = 652782 | 68 (0.860) | 15 (0.220) | 14/250 | 5.9 | 33.9% | coding (1961/1962 nt) | ctpL | methyl‑accepting chemotaxis protein CtpL |
| ? | NC_002947_CJ‑RC | = 4809862 | 0 (0.000) | intergenic (‑268/‑287) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 | |||||
| * | ? | NC_002947_CJ‑RC | = 4809882 | 2 (0.030) | 16 (0.220) | 15/266 | 6.0 | 42.2% | intergenic (‑288/‑267) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947_CJ‑RC | 5991580 = | 42 (0.580) | intergenic (+59/‑487) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947_CJ‑RC | = 4809882 | 2 (0.030) | 11 (0.160) | 10/250 | 7.5 | 25.1% | intergenic (‑288/‑267) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947_CJ‑RC | = 5991764 | 64 (0.940) | intergenic (+243/‑303) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947_CJ‑RC | = 1419549 | 19 (0.240) | 15 (0.190) | 11/284 | 8.0 | 41.9% | intergenic (‑38/+98) | PP_1242/PP_1244 | hypothetical protein/hypothetical protein |
| ? | NC_002947_CJ‑RC | = 1419636 | 23 (0.300) | intergenic (‑125/+11) | PP_1242/PP_1244 | hypothetical protein/hypothetical protein | |||||
| * | ? | NC_002947_CJ‑RC | = 5558423 | 0 (0.000) | 10 (0.130) +GCC |
10/284 | 8.5 | 100% | intergenic (‑84/+87) | PP_4887/PP_4888 | hypothetical protein/methyl‑accepting chemotaxis transducer |
| ? | NC_002947_CJ‑RC | 5558424 = | 0 (0.000) | intergenic (‑85/+86) | PP_4887/PP_4888 | hypothetical protein/methyl‑accepting chemotaxis transducer | |||||
| * | ? | NC_002947_CJ‑RC | 1499510 = | 16 (0.200) | 16 (0.200) +T |
9/288 | 9.1 | 29.8% | intergenic (+87/‑77) | trpS/zapE | tryptophan‑‑tRNA ligase/nucleoside triphosphate hydrolase domain‑containing protein |
| ? | NC_002947_CJ‑RC | = 6063322 | 60 (0.760) | intergenic (+143/+38) | PP_5311/PP_5312 | signal transduction protein/hypothetical protein | |||||
| * | ? | NC_002947_CJ‑RC | = 2957080 | 35 (0.440) | 9 (0.120) | 8/280 | 9.3 | 19.4% | intergenic (+35/‑161) | PP_2588/PP_2589 | class III aminotransferase/aldehyde dehydrogenase family protein |
| ? | NC_002947_CJ‑RC | 2957165 = | 41 (0.540) | intergenic (+120/‑76) | PP_2588/PP_2589 | class III aminotransferase/aldehyde dehydrogenase family protein | |||||
| * | ? | NC_002947_CJ‑RC | 1499510 = | 17 (0.220) | 13 (0.170) +TGGGCGT |
7/276 | 9.7 | 40.0% | intergenic (+87/‑77) | trpS/zapE | tryptophan‑‑tRNA ligase/nucleoside triphosphate hydrolase domain‑containing protein |
| ? | NC_002947_CJ‑RC | = 4891344 | 24 (0.310) | intergenic (+87/‑66) | hyi/glxR | hydroxypyruvate isomerase/2‑hydroxy‑3‑oxopropionate reductase | |||||
| * | ? | NC_002947_CJ‑RC | 1311722 = | 27 (0.340) | 13 (0.170) +ACGCCCA |
7/276 | 9.7 | 38.3% | intergenic (‑190/+88) | PP_1144/rapA | membrane protein/RNA polymerase‑associated protein RapA |
| ? | NC_002947_CJ‑RC | 1499510 = | 17 (0.220) | intergenic (+87/‑77) | trpS/zapE | tryptophan‑‑tRNA ligase/nucleoside triphosphate hydrolase domain‑containing protein | |||||