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 22 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 | 3,466,841 | 0 | T | G | 57.1% | ‑3.5 / 10.3 | 15 | intergenic (‑16/+108) | PP_3081/PP_5560 | hypothetical protein/hypothetical protein |
| * | NC_002947_CJ‑RC | 6,000,018 | 0 | C | G | 55.0% | 11.3 / 26.8 | 20 | intergenic (‑172/+28) | PP_5252/PP_5253 | hypothetical protein/arylesterase |
| * | NC_002947_CJ‑RC | 697,101 | 0 | C | G | 52.9% | ‑2.1 / 13.1 | 18 | intergenic (+28/‑723) | mmsA‑I/PP_16SD | methylmalonate‑semialdehyde dehydrogenase/16S ribosomal RNA |
| * | NC_002947_CJ‑RC | 699,722 | 0 | A | G | 52.7% | 4.0 / 122.5 | 93 | intergenic (+115/‑129) | PP_t06/PP_23SD | tRNA‑Ala/23S ribosomal RNA |
| * | NC_002947_CJ‑RC | 1,840,084 | 0 | T | G | 52.4% | 7.1 / 22.0 | 22 | intergenic (+16/+20) | PP_1646/PP_1647 | thioredoxin/hypothetical protein |
| * | NC_002947_CJ‑RC | 1,327,121 | 0 | C | T | 50.7% | 59.4 / 221.5 | 152 | intergenic (+97/‑196) | PP_16SE/PP_23SE | 16S ribosomal RNA/23S ribosomal RNA |
| * | NC_002947_CJ‑RC | 4,348,812 | 0 | A | G | 49.0% | 36.8 / 148.2 | 102 | intergenic (‑70/+404) | PP_3820/galU | group II intron‑encoding maturase/UTP‑glucose‑1‑phosphate uridylyltransferase |
| * | NC_002947_CJ‑RC | 4,648,338 | 0 | A | C | 41.2% | 46.2 / 10.2 | 34 | V303G (GTG→GGG) | PP_4112 | sulfate transporter |
| * | NC_002947_CJ‑RC | 3,447,291 | 0 | T | G | 41.0% | 24.6 / 12.8 | 42 | A19A (GCT→GCG) | PP_5556 | bacteriophage lysis protein |
| * | NC_002947_CJ‑RC | 4,442,737 | 0 | G | C | 37.5% | 62.6 / 13.7 | 40 | intergenic (‑100/+38) | nicP‑II/nicT | porin‑like protein/metabolite transport protein NicT |
| * | NC_002947_CJ‑RC | 195,634 | 0 | C | T | 34.5% | 142.3 / 100.5 | 116 | T380T (ACC→ACT) | PP_0168 | putative surface adhesion protein |
| * | NC_002947_CJ‑RC | 196,390 | 0 | T | C | 31.8% | 96.5 / 72.6 | 86 | D632D (GAT→GAC) | PP_0168 | putative surface adhesion protein |
| * | NC_002947_CJ‑RC | 1,497,831 | 0 | T | G | 31.7% | 50.6 / 13.4 | 41 | V140G (GTC→GGC) | PP_1310 | hypothetical protein |
| * | NC_002947_CJ‑RC | 3,516,064 | 0 | A | C | 30.0% | 74.2 / 10.1 | 40 | intergenic (+104/‑1031) | PP_5576/PP_5578 | hypothetical protein/hypothetical protein |
| * | NC_002947_CJ‑RC | 196,351 | 0 | C | G | 28.4% | 174.7 / 100.3 | 116 | T619T (ACC→ACG) | PP_0168 | putative surface adhesion protein |
| * | NC_002947_CJ‑RC | 196,327 | 0 | A | C | 26.2% | 208.0 / 110.0 | 126 | T611T (ACA→ACC) | PP_0168 | putative surface adhesion protein |
| * | NC_002947_CJ‑RC | 1,751,059 | 0 | A | G | 26.0% | 92.2 / 11.5 | 56 | T140A (ACC→GCC) | PP_1551 | replication protein O |
| * | NC_002947_CJ‑RC | 5,211,931 | 0 | A | G | 24.4% | 83.1 / 10.3 | 46 | intergenic (‑94/+84) | rnd/PP_4592 | ribonuclease D/metal dependent hydrolase |
| * | NC_002947_CJ‑RC | 196,306 | 0 | T | C | 24.1% | 233.2 / 86.1 | 138 | N604N (AAT→AAC) | PP_0168 | putative surface adhesion protein |
| * | NC_002947_CJ‑RC | 4,442,742 | 0 | G | C | 22.5% | 76.3 / 11.9 | 40 | intergenic (‑105/+33) | nicP‑II/nicT | porin‑like protein/metabolite transport protein NicT |
| Marginal new junction evidence (lowest skew 10 of 47 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_002947_CJ‑RC | = 5558423 | 5 (0.070) | 17 (0.260) +GCC |
16/284 | 4.6 | 77.6% | intergenic (‑84/+87) | PP_4887/PP_4888 | hypothetical protein/methyl‑accepting chemotaxis transducer |
| ? | NC_002947_CJ‑RC | 5558424 = | 5 (0.070) | intergenic (‑85/+86) | PP_4887/PP_4888 | hypothetical protein/methyl‑accepting chemotaxis transducer | |||||
| * | ? | NC_002947_CJ‑RC | 4809877 = | 5 (0.070) | 13 (0.260) | 9/220 | 5.4 | 30.7% | intergenic (‑283/‑272) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947_CJ‑RC | = 5991750 | 55 (1.090) | intergenic (+229/‑317) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947_CJ‑RC | 1737987 = | 66 (0.990) | 9 (0.150) | 9/256 | 6.3 | 10.7% | coding (32/348 nt) | yffB | glutathione‑dependent thiol reductase |
| ? | NC_002947_CJ‑RC | = 1777401 | 92 (1.560) | intergenic (+135/+157) | PP_5476/PP_1585 | hypothetical protein/antidote protein | |||||
| * | ? | NC_002947_CJ‑RC | = 4809882 | 4 (0.060) | 12 (0.200) | 9/266 | 6.6 | 35.5% | intergenic (‑288/‑267) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947_CJ‑RC | 5991580 = | 40 (0.650) | intergenic (+59/‑487) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947_CJ‑RC | = 2957080 | 26 (0.390) | 12 (0.190) | 9/280 | 6.9 | 25.2% | intergenic (+35/‑161) | PP_2588/PP_2589 | class III aminotransferase/aldehyde dehydrogenase family protein |
| ? | NC_002947_CJ‑RC | 2957165 = | 46 (0.710) | intergenic (+120/‑76) | PP_2588/PP_2589 | class III aminotransferase/aldehyde dehydrogenase family protein | |||||
| * | ? | NC_002947_CJ‑RC | = 5290102 | 39 (0.580) | 7 (0.110) | 7/272 | 7.6 | 8.8% | intergenic (‑80/+104) | PP_4660/mdaB | LysR family transcriptional regulator/drug activity modulator B |
| ? | NC_002947_CJ‑RC | 5290245 = | 109 (1.740) | coding (633/672 nt) | mdaB | drug activity modulator B | |||||
| * | ? | NC_002947_CJ‑RC | 5290097 = | 44 (0.660) | 5 (0.090) | 5/230 | 7.6 | 12.5% | intergenic (‑75/+109) | PP_4660/mdaB | LysR family transcriptional regulator/drug activity modulator B |
| ? | NC_002947_CJ‑RC | 5290191 = | 35 (0.660) | intergenic (‑169/+15) | PP_4660/mdaB | LysR family transcriptional regulator/drug activity modulator B | |||||
| * | ? | NC_002947_CJ‑RC | 4079414 = | 37 (0.550) | 6 (0.110) | 5/242 | 7.9 | 18.2% | intergenic (‑218/+166) | sdaC/amaC | serine:H+ symport permease/D‑lysine aminotransferase |
| ? | NC_002947_CJ‑RC | 4079531 = | 23 (0.410) | intergenic (‑335/+49) | sdaC/amaC | serine:H+ symport permease/D‑lysine aminotransferase | |||||
| * | ? | NC_002947_CJ‑RC | = 1419549 | 17 (0.250) | 8 (0.120) | 7/284 | 7.9 | 31.0% | intergenic (‑38/+98) | PP_1242/PP_1244 | hypothetical protein/hypothetical protein |
| ? | NC_002947_CJ‑RC | = 1419636 | 19 (0.290) | intergenic (‑125/+11) | PP_1242/PP_1244 | hypothetical protein/hypothetical protein | |||||
| * | ? | NC_002947_CJ‑RC | = 4982286 | 5 (0.080) | 7 (0.110) +GGG |
6/280 | 8.3 | 58.7% | intergenic (‑22/+46) | PP_4387/flgE | hypothetical protein/flagellar hook protein FlgE |
| ? | NC_002947_CJ‑RC | 4982287 = | 5 (0.070) | intergenic (‑23/+45) | PP_4387/flgE | hypothetical protein/flagellar hook protein FlgE | |||||