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 74 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 3,705,984 | 0 | T | G | 42.0% | 270.3 / inf | 238 | 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 | 42.0% | 223.0 / 298.8 | 238 | intergenic (‑195/+113) | dppB/dppA | dipeptide/heme ABC transporter permease/dipeptide/heme ABC transporter periplasmic binding protein; dipeptide chemotaxis receptor |
| * | NC_000913 | 1,634,946 | 0 | G | T | 37.0% | 49.7 / 27.9 | 27 | A301D (GCT→GAT) | stfQ | Qin prophage; putative side tail fibre assembly protein |
| * | NC_000913 | 1,634,949 | 0 | G | C | 37.0% | 49.9 / 29.5 | 27 | A300G (GCT→GGT) | stfQ | Qin prophage; putative side tail fibre assembly protein |
| * | NC_000913 | 3,706,048 | 0 | G | T | 36.2% | 374.7 / 256.4 | 238 | intergenic (‑258/+50) | dppB/dppA | dipeptide/heme ABC transporter permease/dipeptide/heme ABC transporter periplasmic binding protein; dipeptide chemotaxis receptor |
| * | NC_000913 | 3,706,017 | 0 | C | T | 32.9% | 334.5 / 191.2 | 231 | intergenic (‑227/+81) | 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 | 30.5% | 352.1 / 167.3 | 203 | intergenic (‑180/+128) | 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 | 30.5% | 424.9 / 196.5 | 203 | intergenic (‑181/+127) | 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 | 28.6% | 413.3 / 206.4 | 241 | intergenic (‑188/+120) | dppB/dppA | dipeptide/heme ABC transporter permease/dipeptide/heme ABC transporter periplasmic binding protein; dipeptide chemotaxis receptor |
| * | NC_000913 | 1,634,958 | 0 | G | C | 24.4% | 100.4 / 27.7 | 41 | T297S (ACC→AGC) | stfQ | Qin prophage; putative side tail fibre assembly protein |
| * | NC_000913 | 2,560,321 | 0 | C | T | 24.3% | 265.6 / 84.0 | 140 | A22V (GCT→GTT) | yffL | CPZ‑55 prophage; uncharacterized protein |
| * | NC_000913 | 4,472,434 | 0 | G | A | 24.1% | 242.8 / 73.3 | 133 | R34* (CGA→TGA) | pyrL | pyrBI operon leader peptide |
| * | NC_000913 | 1,674,958 | 0 | A | T | 23.7% | 221.0 / 76.0 | 114 | intergenic (+11/+14) | tqsA/pntB | pheromone AI‑2 transporter/pyridine nucleotide transhydrogenase, beta subunit |
| * | NC_000913 | 681,694 | 0 | A | G | 23.6% | 224.3 / 72.8 | 123 | intergenic (+31/+29) | djlC/hscC | J domain‑containing HscC co‑chaperone; Hsc56/Hsp70 family chaperone Hsc62; RpoD‑binding transcription inhibitor |
| * | NC_000913 | 4,472,437 | 0 | T | C | 23.5% | 226.4 / 79.5 | 132 | N33D (AAT→GAT) | pyrL | pyrBI operon leader peptide |
| * | NC_000913 | 1,634,961 | 0 | A | C | 23.3% | 100.2 / 27.8 | 43 | I296S (ATC→AGC) | stfQ | Qin prophage; putative side tail fibre assembly protein |
| * | NC_000913 | 2,560,326 | 0 | A | G | 23.1% | 284.4 / 88.3 | 148 | T24A (ACA→GCA) | yffL | CPZ‑55 prophage; uncharacterized protein |
| * | NC_000913 | 2,560,317 | 0 | A | C | 23.0% | 322.3 / 104.4 | 148 | N21H (AAT→CAT) | yffL | CPZ‑55 prophage; uncharacterized protein |
| * | NC_000913 | 3,810,324 | 0 | G | A | 22.9% | 184.0 / 50.7 | 96 | intergenic (+20/+19) | coaD/mutM | pantetheine‑phosphate adenylyltransferase/formamidopyrimidine/5‑formyluracil/ 5‑hydroxymethyluracil DNA glycosylase |
| * | NC_000913 | 1,674,955 | 0 | A | T | 22.8% | 231.5 / 71.1 | 115 | intergenic (+8/+17) | tqsA/pntB | pheromone AI‑2 transporter/pyridine nucleotide transhydrogenase, beta subunit |
| Marginal new junction evidence (lowest skew 10 of 518 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 225889 = | NA (NA) | 52 (0.460) | 18/184 | 10.0 | 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 | 225154 = | NA (NA) | 45 (0.390) | 18/188 | 10.3 | NA | noncoding (1384/1542 nt) | rrsH | 16S ribosomal RNA of rrnH operon |
| ? | NC_000913 | 225176 = | NA (NA) | noncoding (1406/1542 nt) | rrsH | 16S ribosomal RNA of rrnH operon | |||||
| * | ? | NC_000913 | 2728214 = | NA (NA) | 54 (0.460) | 18/190 | 10.4 | NA | noncoding (971/2904 nt) | rrlG | 23S ribosomal RNA of rrnG operon |
| ? | NC_000913 | 2728240 = | NA (NA) | noncoding (945/2904 nt) | rrlG | 23S ribosomal RNA of rrnG operon | |||||
| * | ? | NC_000913 | = 226707 | 0 (0.000) | 54 (0.460) | 18/190 | 10.4 | 100% | noncoding (949/2904 nt) | rrlH | 23S ribosomal RNA of rrnH operon |
| ? | NC_000913 | = 226725 | NA (NA) | noncoding (967/2904 nt) | rrlH | 23S ribosomal RNA of rrnH operon | |||||
| * | ? | NC_000913 | 3943467 = | NA (NA) | 49 (0.430) | 17/186 | 10.6 | 58.5% | noncoding (33/76 nt) | gltU | tRNA‑Glu |
| ? | NC_000913 | 3943474 = | 37 (0.310) | noncoding (40/76 nt) | gltU | tRNA‑Glu | |||||
| * | ? | NC_000913 | = 2304902 | NA (NA) | 18 (0.220) +33 bp |
9/132 | 10.7 | NA | noncoding (486/655 nt) | REP161 (repetitive extragenic palindromic) element; contains 12 REP sequences | REP161 (repetitive extragenic palindromic) element; contains 12 REP sequences |
| ? | NC_000913 | = 2305065 | NA (NA) | noncoding (649/655 nt) | REP161 (repetitive extragenic palindromic) element; contains 12 REP sequences | REP161 (repetitive extragenic palindromic) element; contains 12 REP sequences | |||||
| * | ? | NC_000913 | 225078 = | NA (NA) | 41 (0.360) | 16/184 | 10.9 | NA | noncoding (1308/1542 nt) | rrsH | 16S ribosomal RNA of rrnH operon |
| ? | NC_000913 | 225100 = | NA (NA) | noncoding (1330/1542 nt) | rrsH | 16S ribosomal RNA of rrnH operon | |||||
| * | ? | NC_000913 | 4168398 = | 26 (0.210) | 48 (0.420) | 16/186 | 11.0 | 66.3% | noncoding (27/76 nt) | gltT | tRNA‑Glu |
| ? | NC_000913 | 4209819 = | NA (NA) | noncoding (46/76 nt) | gltV | tRNA‑Glu | |||||
| * | ? | NC_000913 | = 3946688 | 133 (1.100) | 91 (0.800) | 16/186 | 11.0 | 42.2% | intergenic (+81/‑12) | rrlC/rrfC | 23S ribosomal RNA of rrnC operon/5S ribosomal RNA of rrnC operon |
| ? | NC_000913 | = 4171601 | NA (NA) | intergenic (+57/‑36) | rrlB/rrfB | 23S ribosomal RNA of rrnB operon/5S ribosomal RNA of rrnB operon | |||||
| * | ? | NC_000913 | = 2729418 | 26 (0.210) | 49 (0.430) | 16/186 | 11.0 | 66.8% | noncoding (27/76 nt) | gltW | tRNA‑Glu |
| ? | NC_000913 | 3943480 = | NA (NA) | noncoding (46/76 nt) | gltU | tRNA‑Glu | |||||