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 33 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 | 1,327,121 | 0 | C | T | 60.5% | 7.7 / 140.6 | 124 | intergenic (+97/‑196) | PP_16SE/PP_23SE | 16S ribosomal RNA/23S ribosomal RNA |
| * | NC_002947_CJ‑RC | 813,350 | 0 | A | . | 60.0% | 20.9 / 151.7 | 70 | intergenic (‑50/+46) | PP_t70/PP_0700 | tRNA‑Met/transmembrane sensor |
| * | NC_002947_CJ‑RC | 3,147,934 | 0 | G | A | 59.5% | 44.3 / 87.2 | 79 | intergenic (‑66/‑129) | sfnA/msuE | acyl‑CoA dehydrogenase/oxidase family protein/FMN reductase |
| * | NC_002947_CJ‑RC | 3,052,341 | 0 | G | . | 59.3% | 11.0 / 123.7 | 59 | coding (1041/1899 nt) | PP_2664 | two‑component system sensor histidine kinase/response regulator |
| * | NC_002947_CJ‑RC | 699,722 | 0 | A | G | 56.9% | 13.7 / 85.4 | 72 | intergenic (+115/‑129) | PP_t06/PP_23SD | tRNA‑Ala/23S ribosomal RNA |
| * | NC_002947_CJ‑RC | 4,809,883 | 0 | A | C | 50.0% | ‑5.4 / 16.6 | 12 | intergenic (‑289/‑266) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| * | NC_002947_CJ‑RC | 4,809,884 | 0 | A | G | 50.0% | ‑6.6 / 11.9 | 12 | intergenic (‑290/‑265) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| * | NC_002947_CJ‑RC | 5,658,451 | 0 | C | A | 50.0% | ‑6.4 / 28.0 | 22 | intergenic (‑91/+61) | epd/tktA | D‑erythrose 4‑phosphate dehydrogenase/transketolase A |
| * | NC_002947_CJ‑RC | 4,348,812 | 0 | A | G | 48.8% | 43.3 / 180.2 | 121 | intergenic (‑70/+404) | PP_3820/galU | group II intron‑encoding maturase/UTP‑glucose‑1‑phosphate uridylyltransferase |
| * | NC_002947_CJ‑RC | 5,658,446 | 0 | T | G | 47.4% | ‑1.6 / 30.3 | 19 | intergenic (‑86/+66) | epd/tktA | D‑erythrose 4‑phosphate dehydrogenase/transketolase A |
| * | NC_002947_CJ‑RC | 195,634 | 0 | C | T | 41.5% | 73.2 / 107.0 | 96 | T380T (ACC→ACT) | PP_0168 | putative surface adhesion protein |
| * | NC_002947_CJ‑RC | 195,559 | 0 | C | A | 38.7% | 87.8 / 53.5 | 63 | T355T (ACC→ACA) | PP_0168 | putative surface adhesion protein |
| * | NC_002947_CJ‑RC | 5,658,456 | 0 | T | . | 37.5% | 39.0 / 31.7 | 24 | intergenic (‑96/+56) | epd/tktA | D‑erythrose 4‑phosphate dehydrogenase/transketolase A |
| * | NC_002947_CJ‑RC | 5,400,171 | 0 | T | C | 36.8% | 52.6 / 68.6 | 68 | I123T (ATT→ACT) | hsdS | type I restriction modification system specificity protein |
| * | NC_002947_CJ‑RC | 1,635,219 | 0 | C | T | 32.3% | 83.9 / 51.4 | 65 | S158S (TCC→TCT) | era | GTPase Era |
| * | NC_002947_CJ‑RC | 5,658,441 | 1 | . | A | 30.8% | 19.1 / 16.3 | 13 | intergenic (‑81/+71) | epd/tktA | D‑erythrose 4‑phosphate dehydrogenase/transketolase A |
| * | NC_002947_CJ‑RC | 251,249 | 0 | A | C | 30.0% | 65.4 / 13.6 | 40 | intergenic (‑47/‑19) | nfeD/PP_0201 | membrane bound peptidase NefD/hypothetical protein |
| * | NC_002947_CJ‑RC | 1,007,524 | 0 | G | T | 30.0% | 50.6 / 11.0 | 30 | intergenic (+24/+66) | PP_0867/yehX | FecA‑like outer membrane receptor/ABC transporter ATP‑binding protein |
| * | NC_002947_CJ‑RC | 1,013,249 | 0 | T | G | 28.6% | 34.6 / 16.9 | 21 | intergenic (+77/+54) | prfC/potF‑I | peptide chain release factor 3/putrescine‑binding protein |
| * | NC_002947_CJ‑RC | 1,013,248 | 0 | A | T | 27.3% | 34.3 / 12.8 | 22 | intergenic (+76/+55) | prfC/potF‑I | peptide chain release factor 3/putrescine‑binding protein |
| Marginal new junction evidence (lowest skew 10 of 19 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_002947_CJ‑RC | 4809877 = | 9 (0.140) | 13 (0.260) | 9/222 | 5.7 | 39.5% | intergenic (‑283/‑272) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947_CJ‑RC | = 5991750 | 33 (0.660) | intergenic (+229/‑317) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947_CJ‑RC | = 5558423 | 2 (0.030) | 14 (0.220) +GCC |
12/286 | 6.2 | 87.7% | intergenic (‑84/+87) | PP_4887/PP_4888 | hypothetical protein/methyl‑accepting chemotaxis transducer |
| ? | NC_002947_CJ‑RC | 5558424 = | 2 (0.030) | intergenic (‑85/+86) | PP_4887/PP_4888 | hypothetical protein/methyl‑accepting chemotaxis transducer | |||||
| * | ? | NC_002947_CJ‑RC | = 5684230 | 1 (0.020) | 13 (0.200) +CGGG |
11/284 | 6.5 | 93.0% | intergenic (‑133/+71) | PP_4986/PP_4987 | hemolysin III family channel protein/putative Chemotaxis protein |
| ? | NC_002947_CJ‑RC | 5684231 = | 1 (0.020) | intergenic (‑134/+70) | PP_4986/PP_4987 | hemolysin III family channel protein/putative Chemotaxis protein | |||||
| * | ? | NC_002947_CJ‑RC | = 2957080 | 40 (0.610) | 9 (0.140) | 9/282 | 7.3 | 16.9% | intergenic (+35/‑161) | PP_2588/PP_2589 | class III aminotransferase/aldehyde dehydrogenase family protein |
| ? | NC_002947_CJ‑RC | 2957165 = | 50 (0.790) | intergenic (+120/‑76) | PP_2588/PP_2589 | class III aminotransferase/aldehyde dehydrogenase family protein | |||||
| * | ? | NC_002947_CJ‑RC | = 5991586 | 47 (0.710) | 6 (0.100) | 6/276 | 8.6 | 11.9% | intergenic (+65/‑481) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA |
| ? | NC_002947_CJ‑RC | 5991778 = | 44 (0.710) | intergenic (+257/‑289) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947_CJ‑RC | = 2472115 | 18 (0.270) | 6 (0.100) | 6/278 | 8.6 | 15.4% | intergenic (+19/+130) | PP_2166/PP_2167 | anti‑anti‑sigma factor/PhoD‑like phosphatase |
| ? | NC_002947_CJ‑RC | 2472313 = | 49 (0.780) | coding (1783/1851 nt) | PP_2167 | PhoD‑like phosphatase | |||||
| * | ? | NC_002947_CJ‑RC | 2050559 = | 22 (0.330) | 3 (0.060) | 3/218 | 8.9 | 13.5% | intergenic (‑52/+123) | PP_1824/PP_1825 | Smr domain‑containing protein/hypothetical protein |
| ? | NC_002947_CJ‑RC | 2050669 = | 22 (0.450) | intergenic (‑162/+13) | PP_1824/PP_1825 | Smr domain‑containing protein/hypothetical protein | |||||
| * | ? | NC_002947_CJ‑RC | = 1780066 | 10 (0.150) | 5 (0.080) | 5/278 | 9.2 | 31.7% | intergenic (+25/+81) | PP_1587/dapC | NhaP‑type Na+(K+)/H+ antiporter/N‑succinyl‑L,L‑diaminopimelate aminotransferase |
| ? | NC_002947_CJ‑RC | 1780129 = | 12 (0.190) | intergenic (+88/+18) | PP_1587/dapC | NhaP‑type Na+(K+)/H+ antiporter/N‑succinyl‑L,L‑diaminopimelate aminotransferase | |||||
| * | ? | NC_002947_CJ‑RC | 5290097 = | 29 (0.440) | 4 (0.080) | 3/232 | 9.3 | 15.4% | intergenic (‑75/+109) | PP_4660/mdaB | LysR family transcriptional regulator/drug activity modulator B |
| ? | NC_002947_CJ‑RC | 5290191 = | 21 (0.400) | intergenic (‑169/+15) | PP_4660/mdaB | LysR family transcriptional regulator/drug activity modulator B | |||||
| * | ? | NC_002947_CJ‑RC | = 5391054 | 74 (1.120) | 3 (0.060) | 3/238 | 9.5 | 4.3% | intergenic (+50/‑270) | dld2/PP_4738 | D‑lactate dehydrogenase/hypothetical protein |
| ? | NC_002947_CJ‑RC | = 5391109 | 73 (1.360) | intergenic (+105/‑215) | dld2/PP_4738 | D‑lactate dehydrogenase/hypothetical protein | |||||