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 54 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 4,296,060 | 0 | C | T | 31.3% | 254.1 / 168.4 | 195 | intergenic (+266/+376) | gltP/yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| * | NC_000913 | 4,051,259 | 0 | G | T | 25.9% | 271.8 / 102.5 | 131 | noncoding (224/245 nt) | csrC | CsrC sRNA sequesters CsrA, a carbon flux regulator |
| * | NC_000913 | 2,800,519 | 0 | T | G | 24.8% | 224.9 / 85.1 | 117 | intergenic (+44/‑204) | ygaM/nrdH | putative membrane‑anchored DUF883 family ribosome‑binding protein/hydrogen donor for NrdEF electron transport system; glutaredoxin‑like protein |
| * | NC_000913 | 4,051,262 | 0 | A | C | 24.1% | 293.4 / 104.0 | 141 | noncoding (227/245 nt) | csrC | CsrC sRNA sequesters CsrA, a carbon flux regulator |
| * | NC_000913 | 3,171,863 | 0 | A | G | 23.8% | 242.9 / 82.7 | 130 | intergenic (+30/+16) | qseC/ygiZ | quorum sensing sensory histidine kinase in two‑component regulatory system with QseB/inner membrane protein |
| * | NC_000913 | 2,286,313 | 0 | T | A | 23.7% | 273.8 / 88.1 | 137 | intergenic (+26/+77) | proL/yejO | tRNA‑Pro/pseudogene, autotransporter outer membrane homology;putative transport; Not classified; putative ATP‑binding component of a transport system |
| * | NC_000913 | 3,202,686 | 0 | C | T | 23.7% | 340.7 / 106.3 | 173 | L266F (CTC→TTC) | cca | fused tRNA nucleotidyl transferase/2'3'‑cyclic phosphodiesterase/2'nucleotidase and phosphatase |
| * | NC_000913 | 1,865,682 | 0 | G | C | 23.7% | 373.1 / 120.7 | 169 | intergenic (‑46/+44) | yeaE/mipA | aldo‑keto reductase, methylglyoxal to acetol, NADPH‑dependent/scaffolding protein for murein synthesizing machinery |
| * | NC_000913 | 4,307,290 | 0 | T | C | 23.5% | 246.8 / 76.9 | 133 | G170G (GGA→GGG) | alsK | D‑allose kinase |
| * | NC_000913 | 3,202,685 | 0 | A | G | 23.4% | 339.7 / 108.8 | 175 | E265E (GAA→GAG) | cca | fused tRNA nucleotidyl transferase/2'3'‑cyclic phosphodiesterase/2'nucleotidase and phosphatase |
| * | NC_000913 | 120,154 | 0 | T | . | 23.4% | 356.5 / 105.7 | 124 | intergenic (+19/+24) | ampE/aroP | ampicillin resistance inner membrane protein; putative signaling protein in beta‑lactamase regulation/aromatic amino acid transporter |
| * | NC_000913 | 2,286,311 | 0 | C | G | 23.4% | 304.2 / 97.2 | 137 | intergenic (+24/+79) | proL/yejO | tRNA‑Pro/pseudogene, autotransporter outer membrane homology;putative transport; Not classified; putative ATP‑binding component of a transport system |
| * | NC_000913 | 2,286,315 | 0 | C | G | 23.4% | 308.1 / 97.4 | 137 | intergenic (+28/+75) | proL/yejO | tRNA‑Pro/pseudogene, autotransporter outer membrane homology;putative transport; Not classified; putative ATP‑binding component of a transport system |
| * | NC_000913 | 2,800,515 | 0 | C | A | 23.3% | 251.7 / 75.3 | 116 | intergenic (+40/‑208) | ygaM/nrdH | putative membrane‑anchored DUF883 family ribosome‑binding protein/hydrogen donor for NrdEF electron transport system; glutaredoxin‑like protein |
| * | NC_000913 | 120,158 | 1 | . | A | 23.2% | 300.6 / 131.7 | 125 | intergenic (+23/+20) | ampE/aroP | ampicillin resistance inner membrane protein; putative signaling protein in beta‑lactamase regulation/aromatic amino acid transporter |
| * | NC_000913 | 2,356,737 | 0 | T | C | 23.2% | 241.7 / 73.5 | 125 | intergenic (+26/‑167) | glpC/yfaD | anaerobic sn‑glycerol‑3‑phosphate dehydrogenase, C subunit, 4Fe‑4S iron‑sulfur cluster/transposase_31 family protein |
| * | NC_000913 | 3,171,852 | 0 | C | T | 23.1% | 262.9 / 77.1 | 131 | intergenic (+19/+27) | qseC/ygiZ | quorum sensing sensory histidine kinase in two‑component regulatory system with QseB/inner membrane protein |
| * | NC_000913 | 1,674,958 | 0 | A | T | 22.9% | 276.8 / 85.4 | 131 | intergenic (+11/+14) | tqsA/pntB | pheromone AI‑2 transporter/pyridine nucleotide transhydrogenase, beta subunit |
| * | NC_000913 | 2,323,280 | 0 | A | G | 22.9% | 362.2 / 94.5 | 166 | intergenic (+29/‑167) | atoC/atoD | fused response regulator of ato operon, in two‑component system with AtoS: response regulator/sigma54 interaction protein/acetyl‑CoA:acetoacetyl‑CoA transferase, alpha subunit |
| * | NC_000913 | 2,800,517 | 0 | T | A | 22.9% | 243.7 / 78.1 | 118 | intergenic (+42/‑206) | ygaM/nrdH | putative membrane‑anchored DUF883 family ribosome‑binding protein/hydrogen donor for NrdEF electron transport system; glutaredoxin‑like protein |
| Marginal new junction evidence (lowest skew 10 of 1256 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 1468681 | NA (NA) | 109 (1.540) +44 bp |
15/110 | 5.6 | NA | noncoding (560/1331 nt) | IS2 | repeat region |
| ? | NC_000913 | 1650843 = | NA (NA) | noncoding (1/706 nt) | IS2 | repeat region | |||||
| * | ? | NC_000913 | 381819 = | NA (NA) | 45 (0.380) | 16/184 | 10.9 | NA | noncoding (560/1331 nt) | IS2 | repeat region |
| ? | NC_000913 | 381841 = | NA (NA) | noncoding (582/1331 nt) | IS2 | repeat region | |||||
| * | ? | NC_000913 | = 3718305 | 116 (0.900) | 21 (0.180) | 15/182 | 11.2 | 15.9% | intergenic (+21/+29) | ghrB/yiaF | glyoxylate/hydroxypyruvate reductase B/barrier effect co‑colonization resistance factor; DUF3053 family lipoprotein |
| ? | NC_000913 | = 3718325 | 115 (0.970) | intergenic (+41/+9) | ghrB/yiaF | glyoxylate/hydroxypyruvate reductase B/barrier effect co‑colonization resistance factor; DUF3053 family lipoprotein | |||||
| * | ? | NC_000913 | = 2947467 | 94 (0.730) | 12 (0.160) +40 bp |
6/118 | 11.3 | 15.6% | intergenic (+4/‑30) | metZ/metW | tRNA‑Met/tRNA‑Met |
| ? | NC_000913 | = 2947757 | 125 (0.970) | coding (1254/1254 nt) | amiC | N‑acetylmuramoyl‑L‑alanine amidase | |||||
| * | ? | NC_000913 | = 3546221 | NA (NA) | 30 (0.250) | 15/186 | 11.5 | NA | intergenic (+22/‑338) | nfuA/gntT | Fe/S biogenesis protein, putative scaffold/chaperone protein/gluconate transporter, high‑affinity GNT I system |
| ? | NC_000913 | = 3546253 | NA (NA) | noncoding (32/36 nt) | REP253 (repetitive extragenic palindromic) element; contains 1 REP sequences | REP253 (repetitive extragenic palindromic) element; contains 1 REP sequences | |||||
| * | ? | NC_000913 | = 2464223 | 141 (1.100) | 20 (0.180) | 13/172 | 11.5 | 13.6% | intergenic (+153/+29) | yfdF/mlaA | uncharacterized protein/ABC transporter maintaining OM lipid asymmetry, OM lipoprotein component |
| ? | NC_000913 | = 2464229 | 132 (1.180) | intergenic (+159/+23) | yfdF/mlaA | uncharacterized protein/ABC transporter maintaining OM lipid asymmetry, OM lipoprotein component | |||||
| * | ? | NC_000913 | = 227444 | NA (NA) | 24 (0.200) | 15/188 | 11.6 | NA | noncoding (1686/2904 nt) | rrlH | 23S ribosomal RNA of rrnH operon |
| ? | NC_000913 | = 227459 | NA (NA) | noncoding (1701/2904 nt) | rrlH | 23S ribosomal RNA of rrnH operon | |||||
| * | ? | NC_000913 | 225889 = | NA (NA) | 45 (0.380) | 14/184 | 11.9 | 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 | = 315646 | NA (NA) | 32 (0.260) | 14/188 | 12.1 | NA | noncoding (418/1255 nt) | IS3 | repeat region |
| ? | NC_000913 | = 315665 | NA (NA) | noncoding (437/1255 nt) | IS3 | repeat region | |||||
| * | ? | NC_000913 | 2728214 = | NA (NA) | 52 (0.420) | 14/190 | 12.3 | 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 | |||||