mutation predictions | marginal predictions | summary statistics | genome diff | command line log
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breseq version 0.29.0 revision 8f9c342918e4
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Marginal read alignment evidence (highest frequency 20 of 135 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 3,705,984 | 0 | T | G | 43.9% | 262.9 / inf | 278 | intergenic (‑194/+114) | dppB/dppA | dipeptide/heme ABC transporter permease/dipeptide/heme ABC transporter periplasmic binding protein; dipeptide chemotaxis receptor |
| * | NC_000913 | 3,705,985 | 0 | T | C | 43.9% | 217.7 / inf | 278 | intergenic (‑195/+113) | dppB/dppA | dipeptide/heme ABC transporter permease/dipeptide/heme ABC transporter periplasmic binding protein; dipeptide chemotaxis receptor |
| * | NC_000913 | 3,706,048 | 0 | G | T | 40.2% | 320.9 / 312.5 | 263 | intergenic (‑258/+50) | dppB/dppA | dipeptide/heme ABC transporter permease/dipeptide/heme ABC transporter periplasmic binding protein; dipeptide chemotaxis receptor |
| * | NC_000913 | 2,644,289 | 0 | A | C | 35.3% | 192.2 / 214.0 | 190 | intergenic (‑6/+144) | rlmN/ndk | dual specificity 23S rRNA m(2)A2503, tRNA m(2)A37 methyltransferase, SAM‑dependent/multifunctional nucleoside diphosphate kinase and apyrimidinic endonuclease and 3'‑phosphodiesterase |
| * | NC_000913 | 3,706,017 | 0 | C | T | 35.1% | 332.2 / 229.4 | 269 | intergenic (‑227/+81) | dppB/dppA | dipeptide/heme ABC transporter permease/dipeptide/heme ABC transporter periplasmic binding protein; dipeptide chemotaxis receptor |
| * | NC_000913 | 3,705,971 | 0 | C | A | 33.5% | 364.5 / 219.8 | 213 | intergenic (‑181/+127) | dppB/dppA | dipeptide/heme ABC transporter permease/dipeptide/heme ABC transporter periplasmic binding protein; dipeptide chemotaxis receptor |
| * | NC_000913 | 3,705,970 | 0 | G | A | 32.9% | 313.7 / 189.0 | 213 | intergenic (‑180/+128) | dppB/dppA | dipeptide/heme ABC transporter permease/dipeptide/heme ABC transporter periplasmic binding protein; dipeptide chemotaxis receptor |
| * | NC_000913 | 3,705,978 | 0 | A | C | 31.9% | 389.1 / 262.1 | 278 | intergenic (‑188/+120) | dppB/dppA | dipeptide/heme ABC transporter permease/dipeptide/heme ABC transporter periplasmic binding protein; dipeptide chemotaxis receptor |
| * | NC_000913 | 4,296,060 | 0 | C | T | 28.9% | 317.5 / 128.3 | 198 | intergenic (+266/+376) | gltP/yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| * | NC_000913 | 1,520,080 | 0 | G | T | 28.4% | 300.3 / 141.7 | 177 | intergenic (+16/‑182) | curA/mcbR | curcumin/dihydrocurcumin reductase, NADPH‑dependent/colanic acid and biofilm gene transcriptional regulator, MqsR‑controlled |
| * | NC_000913 | 603,393 | 0 | T | A | 27.6% | 233.7 / 106.7 | 145 | intergenic (+58/+23) | pheP/ybdG | phenylalanine transporter/mechanosensitive channel protein, miniconductance |
| * | NC_000913 | 603,395 | 0 | C | G | 27.4% | 257.8 / 120.0 | 146 | intergenic (+60/+21) | pheP/ybdG | phenylalanine transporter/mechanosensitive channel protein, miniconductance |
| * | NC_000913 | 1,520,083 | 0 | A | C | 27.3% | 288.2 / 149.5 | 184 | intergenic (+19/‑179) | curA/mcbR | curcumin/dihydrocurcumin reductase, NADPH‑dependent/colanic acid and biofilm gene transcriptional regulator, MqsR‑controlled |
| * | NC_000913 | 603,391 | 0 | C | G | 27.2% | 264.0 / 120.2 | 147 | intergenic (+56/+25) | pheP/ybdG | phenylalanine transporter/mechanosensitive channel protein, miniconductance |
| * | NC_000913 | 1,674,958 | 0 | A | T | 27.2% | 243.8 / 113.7 | 151 | intergenic (+11/+14) | tqsA/pntB | pheromone AI‑2 transporter/pyridine nucleotide transhydrogenase, beta subunit |
| * | NC_000913 | 1,674,955 | 0 | A | T | 27.0% | 243.4 / 115.0 | 152 | intergenic (+8/+17) | tqsA/pntB | pheromone AI‑2 transporter/pyridine nucleotide transhydrogenase, beta subunit |
| * | NC_000913 | 3,706,029 | 0 | T | C | 26.5% | 414.0 / 171.5 | 271 | intergenic (‑239/+69) | dppB/dppA | dipeptide/heme ABC transporter permease/dipeptide/heme ABC transporter periplasmic binding protein; dipeptide chemotaxis receptor |
| * | NC_000913 | 3,714,163 | 1 | . | T | 25.9% | 272.2 / 151.1 | 135 | coding (2232/2334 nt) | bisC | biotin sulfoxide reductase |
| * | NC_000913 | 4,060,261 | 0 | G | T | 25.5% | 281.9 / 104.3 | 149 | intergenic (+31/‑186) | typA/yihL | GTP‑binding protein/putative DNA‑binding transcriptional regulator |
| * | NC_000913 | 3,714,168 | 0 | A | . | 24.6% | 359.0 / 122.5 | 143 | coding (2227/2334 nt) | bisC | biotin sulfoxide reductase |
| Marginal new junction evidence (lowest skew 10 of 1429 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 1207790 = | 129 (0.950) | 30 (0.260) | 28/166 | 7.2 | 23.3% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | 1209619 = | 90 (0.790) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 132 (0.970) | 23 (0.200) | 21/166 | 9.8 | 19.1% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | = 1209602 | 85 (0.750) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 228108 | NA (NA) | 66 (0.510) | 24/190 | 10.4 | NA | noncoding (2350/2904 nt) | rrlH | 23S ribosomal RNA of rrnH operon |
| ? | NC_000913 | = 228124 | NA (NA) | noncoding (2366/2904 nt) | rrlH | 23S ribosomal RNA of rrnH operon | |||||
| * | ? | NC_000913 | 225889 = | NA (NA) | 69 (0.550) | 22/184 | 10.8 | NA | noncoding (131/2904 nt) | rrlH | 23S ribosomal RNA of rrnH operon |
| ? | NC_000913 | 225907 = | NA (NA) | noncoding (149/2904 nt) | rrlH | 23S ribosomal RNA of rrnH operon | |||||
| * | ? | NC_000913 | = 4037450 | NA (NA) | 46 (0.360) | 21/184 | 11.2 | 22.1% | intergenic (+115/‑69) | alaT/rrlA | tRNA‑Ala/23S ribosomal RNA of rrnA operon |
| ? | NC_000913 | = 4168568 | 175 (1.290) | intergenic (+121/‑73) | gltT/rrlB | tRNA‑Glu/23S ribosomal RNA of rrnB operon | |||||
| * | ? | NC_000913 | = 225281 | NA (NA) | 73 (0.570) | 21/188 | 11.5 | NA | noncoding (1511/1542 nt) | rrsH | 16S ribosomal RNA of rrnH operon |
| ? | NC_000913 | = 225293 | NA (NA) | noncoding (1523/1542 nt) | rrsH | 16S ribosomal RNA of rrnH operon | |||||
| * | ? | NC_000913 | = 3943624 | NA (NA) | 39 (0.310) | 20/184 | 11.6 | 76.4% | intergenic (+114/‑80) | gltU/rrlC | tRNA‑Glu/23S ribosomal RNA of rrnC operon |
| ? | NC_000913 | = 4037457 | 13 (0.100) | intergenic (+122/‑62) | alaT/rrlA | tRNA‑Ala/23S ribosomal RNA of rrnA operon | |||||
| * | ? | NC_000913 | = 3944978 | NA (NA) | 84 (0.660) | 20/186 | 11.8 | 84.8% | noncoding (1275/2904 nt) | rrlC | 23S ribosomal RNA of rrnC operon |
| ? | NC_000913 | = 4038811 | 16 (0.120) | noncoding (1293/2905 nt) | rrlA | 23S ribosomal RNA of rrnA operon | |||||
| * | ? | NC_000913 | = 1475100 | 131 (0.960) | 29 (0.240) | 18/178 | 12.0 | 19.3% | intergenic (+19/‑44) | ydbC/ydbD | putative NAD(P)‑binding oxidoreductase/PF10971 family putative periplasmic methylglyoxal resistance protein |
| ? | NC_000913 | = 1475106 | 125 (1.020) | intergenic (+25/‑38) | ydbC/ydbD | putative NAD(P)‑binding oxidoreductase/PF10971 family putative periplasmic methylglyoxal resistance protein | |||||
| * | ? | NC_000913 | = 4171625 | 32 (0.240) | 136 (1.060) | 19/186 | 12.2 | 81.9% | intergenic (+81/‑12) | rrlB/rrfB | 23S ribosomal RNA of rrnB operon/5S ribosomal RNA of rrnB operon |
| ? | NC_000913 | = 4213004 | NA (NA) | intergenic (+58/‑36) | rrlE/rrfE | 23S ribosomal RNA of rrnE operon/5S ribosomal RNA of rrnE operon | |||||