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 22 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 3,705,984 | 0 | T | G | 36.1% | 311.6 / 261.7 | 205 | 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 | 36.1% | 273.7 / 219.7 | 205 | 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 | 31.3% | 356.8 / 169.0 | 189 | 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 | 27.7% | 334.9 / 130.6 | 190 | 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 | 26.8% | 351.4 / 129.4 | 180 | 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 | 26.8% | 414.9 / 148.7 | 180 | intergenic (‑181/+127) | 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 | 26.1% | 425.3 / 166.2 | 247 | intergenic (+266/+376) | gltP/yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| * | NC_000913 | 1,634,946 | 0 | G | T | 25.9% | 57.9 / 16.5 | 27 | A301D (GCT→GAT) | stfQ | Qin prophage; putative side tail fibre assembly protein |
| * | NC_000913 | 1,634,949 | 0 | G | C | 25.9% | 59.2 / 18.4 | 27 | A300G (GCT→GGT) | stfQ | Qin prophage; putative side tail fibre assembly protein |
| * | NC_000913 | 3,705,978 | 0 | A | C | 24.3% | 430.3 / 156.8 | 211 | intergenic (‑188/+120) | dppB/dppA | dipeptide/heme ABC transporter permease/dipeptide/heme ABC transporter periplasmic binding protein; dipeptide chemotaxis receptor |
| * | NC_000913 | 2,323,280 | 0 | A | G | 22.6% | 205.3 / 58.1 | 102 | 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 | 2,323,275 | 0 | T | A | 22.2% | 249.3 / 64.5 | 108 | intergenic (+24/‑172) | 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 | 4,051,259 | 0 | G | T | 22.2% | 274.8 / 74.0 | 117 | intergenic (‑494/‑88) | yihA/yihI | cell division GTP‑binding protein/activator of Der GTPase |
| * | NC_000913 | 2,323,283 | 0 | G | C | 21.7% | 262.0 / 69.2 | 107 | intergenic (+32/‑164) | 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 | 3,781,145 | 0 | C | G | 21.6% | 253.7 / 22.9 | 102 | intergenic (+128/‑70) | lldD/trmL | L‑lactate dehydrogenase, FMN‑linked/tRNA Leu mC34,mU34 2'‑O‑methyltransferase, SAM‑dependent |
| * | NC_000913 | 1,232,481 | 0 | C | T | 21.6% | 236.1 / 62.1 | 117 | intergenic (+27/+19) | umuC/dsbB | translesion error‑prone DNA polymerase V subunit; DNA polymerase activity/oxidoreductase that catalyzes reoxidation of DsbA protein disulfide isomerase I |
| * | NC_000913 | 2,323,286 | 0 | C | T | 21.3% | 230.2 / 56.0 | 108 | intergenic (+35/‑161) | 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 | 4,051,262 | 0 | A | C | 21.1% | 274.1 / 79.7 | 123 | intergenic (‑497/‑85) | yihA/yihI | cell division GTP‑binding protein/activator of Der GTPase |
| * | NC_000913 | 3,888,212 | 0 | T | . | 20.3% | 349.6 / 88.6 | 123 | intergenic (+20/‑223) | mnmE/tnaC | tRNA U34 5‑methylaminomethyl‑2‑thiouridine modification GTPase/tryptophanase leader peptide |
| * | NC_000913 | 2,323,291 | 0 | T | A | 20.2% | 275.0 / 62.8 | 114 | intergenic (+40/‑156) | 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 |
| Marginal new junction evidence (lowest skew 10 of 1650 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 1468681 | NA (NA) | 74 (1.110) +44 bp |
8/110 | 9.9 | NA | noncoding (560/1331 nt) | IS2 | repeat region |
| ? | NC_000913 | 1650843 = | NA (NA) | noncoding (1/706 nt) | IS2 | repeat region | |||||
| * | ? | NC_000913 | = 2305015 | 184 (1.520) | 19 (0.240) +33 bp |
11/132 | 10.2 | 13.5% | noncoding (599/655 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 | 2728214 = | NA (NA) | 56 (0.480) | 20/190 | 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) | 56 (0.480) | 20/190 | 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 | 4201782 = | 112 (0.930) | 22 (0.220) | 15/164 | 10.7 | 18.9% | intergenic (‑94/‑144) | zraP/zraS | Zn‑dependent periplasmic chaperone/sensory histidine kinase in two‑component regulatory system with ZraR |
| ? | NC_000913 | 4201828 = | 96 (0.960) | intergenic (‑140/‑98) | zraP/zraS | Zn‑dependent periplasmic chaperone/sensory histidine kinase in two‑component regulatory system with ZraR | |||||
| * | ? | NC_000913 | 2560906 = | 130 (1.070) | 15 (0.170) +27 bp |
11/144 | 11.2 | 13.6% | intergenic (+8/‑462) | yffL/yffM | CPZ‑55 prophage; uncharacterized protein/CPZ‑55 prophage; uncharacterized protein |
| ? | NC_000913 | 2560978 = | 133 (1.100) | intergenic (+80/‑390) | yffL/yffM | CPZ‑55 prophage; uncharacterized protein/CPZ‑55 prophage; uncharacterized protein | |||||
| * | ? | NC_000913 | 225078 = | NA (NA) | 71 (0.630) | 17/184 | 11.2 | 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 | 225154 = | NA (NA) | 31 (0.270) | 17/188 | 11.5 | 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 | = 225998 | NA (NA) | 27 (0.230) | 17/190 | 11.7 | NA | noncoding (240/2904 nt) | rrlH | 23S ribosomal RNA of rrnH operon |
| ? | NC_000913 | = 226015 | NA (NA) | noncoding (257/2904 nt) | rrlH | 23S ribosomal RNA of rrnH operon | |||||
| * | ? | NC_000913 | 225889 = | NA (NA) | 38 (0.340) | 16/184 | 11.7 | 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 | |||||