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 24 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 4,604,344 | 0 | C | T | 43.7% | 83.2 / 75.0 | 103 | S62F (TCT→TTT) | bglJ | DNA‑binding transcriptional regulator BglJ |
| * | NC_000913 | 836,756 | 0 | T | G | 33.3% | 69.0 / 10.9 | 42 | F136V (TTT→GTT) | hcxB | hydroxycarboxylate dehydrogenase B |
| * | NC_000913 | 1,825,061 | 0 | G | A | 32.0% | 77.3 / 14.1 | 50 | intergenic (‑124/+79) | ves/spy | HutD family protein Ves/ATP‑independent periplasmic chaperone |
| * | NC_000913 | 650,809 | 0 | T | G | 30.5% | 98.8 / 15.4 | 60 | T350P (ACC→CCC) | citC | citrate lyase synthetase |
| * | NC_000913 | 4,568,504 | 0 | T | G | 30.1% | 241.8 / 21.3 | 134 | T6P (ACC→CCC) | mdtM | multidrug efflux pump/bile salt:H(+) antiporter/Na(+):H(+) antiporter/K(+):H(+) antiporter |
| * | NC_000913 | 4,111,747 | 0 | G | T | 29.5% | 107.1 / 21.0 | 44 | N156K (AAC→AAA) | yiiQ | DUF1454 domain‑containing protein YiiQ |
| * | NC_000913 | 888,014 | 0 | T | G | 28.7% | 156.7 / 29.6 | 87 | noncoding (44/81 nt) | rybB | small regulatory RNA RybB |
| * | NC_000913 | 802,118 | 0 | A | C | 28.6% | 104.8 / 13.5 | 56 | T78P (ACC→CCC) | ybhI | putative tricarboxylate transporter |
| * | NC_000913 | 4,101,507 | 0 | T | G | 28.4% | 155.9 / 15.5 | 82 | intergenic (+77/‑183) | sodA/kdgT | superoxide dismutase (Mn)/2‑dehydro‑3‑deoxy‑D‑gluconate:H(+) symporter |
| * | NC_000913 | 4,429,984 | 0 | T | G | 26.8% | 148.6 / 19.2 | 71 | L41V (TTG→GTG) | cycA | serine/alanine/glycine/cycloserine:H(+)symporter |
| * | NC_000913 | 4,296,060 | 0 | C | T | 26.7% | 230.9 / 91.1 | 135 | intergenic (+266/+376) | gltP/yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| * | NC_000913 | 29,496 | 0 | T | A | 26.6% | 137.1 / 23.8 | 64 | intergenic (+301/‑155) | dapB/carA | 4‑hydroxy‑tetrahydrodipicolinate reductase/carbamoyl phosphate synthetase subunit alpha |
| * | NC_000913 | 2,628,625 | 0 | A | C | 26.1% | 93.0 / 11.4 | 46 | V105G (GTC→GGC) | pdeF | cyclic di‑GMP phosphodiesterase PdeF |
| * | NC_000913 | 3,404,215 | 0 | T | G | 25.8% | 126.9 / 22.0 | 66 | G244G (GGT→GGG) | yhdH | acrylyl‑CoA reductase |
| * | NC_000913 | 1,491,098 | 0 | A | C | 24.7% | 196.1 / 11.0 | 94 | Y66S (TAC→TCC) | cybB | cytochrome b561 |
| * | NC_000913 | 175,694 | 0 | T | G | 24.7% | 177.1 / 13.0 | 85 | G196G (GGT→GGG) | clcA | chloride:H(+) antiporter ClcA |
| * | NC_000913 | 2,667,126 | 0 | A | C | 23.2% | 183.4 / 11.8 | 84 | Y241D (TAT→GAT) | hcaT | putative 3‑phenylpropionate transporter |
| * | NC_000913 | 3,531,440 | 0 | A | C | 22.9% | 270.9 / 24.0 | 119 | Y334D (TAT→GAT) | yhgE | putative transport protein YhgE |
| * | NC_000913 | 646,747 | 0 | T | G | 22.8% | 124.4 / 18.0 | 57 | T255P (ACC→CCC) | citG | triphosphoribosyl‑dephospho‑CoA synthase |
| * | NC_000913 | 3,404,218 | 0 | T | G | 22.7% | 144.5 / 12.2 | 66 | G245G (GGT→GGG) | yhdH | acrylyl‑CoA reductase |
| Marginal new junction evidence (lowest skew 10 of 12 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 4542682 = | 82 (0.880) | 16 (0.180) | 14/260 | 4.1 | 15.1% | intergenic (+49/‑433) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | 4542996 = | 103 (1.180) | intergenic (+363/‑119) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | = 4542690 | 81 (0.870) | 11 (0.130) | 9/260 | 5.5 | 11.1% | intergenic (+57/‑425) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | = 4542986 | 101 (1.160) | intergenic (+353/‑129) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | = 2728251 | NA (NA) | 8 (0.090) | 6/268 | 6.8 | NA | noncoding (934/2904 nt) | rrlG | 23S ribosomal RNA |
| ? | NC_000913 | = 2728340 | NA (NA) | noncoding (845/2904 nt) | rrlG | 23S ribosomal RNA | |||||
| * | ? | NC_000913 | = 608006 | 74 (0.980) | 6 (0.080) | 3/226 | 7.5 | 7.5% | intergenic (+18/‑59) | hokE/insL‑2 | protein HokE/IS186/IS421 transposase |
| ? | NC_000913 | = 609351 | NA (NA) | noncoding (1345/1345 nt) | IS186 | repeat region | |||||
| * | ? | NC_000913 | 4530896 = | 140 (1.500) | 5 (0.060) | 3/262 | 8.2 | 3.5% | coding (756/1122 nt) | sgcX | KpLE2 phage‑like element; putative endoglucanase with Zn‑dependent exopeptidase domain |
| ? | NC_000913 | 4530971 = | 147 (1.680) | coding (681/1122 nt) | sgcX | KpLE2 phage‑like element; putative endoglucanase with Zn‑dependent exopeptidase domain | |||||
| * | ? | NC_000913 | = 839440 | 67 (0.720) | 3 (0.030) | 3/268 | 8.3 | 4.7% | coding (2092/2283 nt) | fiu | putative iron siderophore outer membrane transporter |
| ? | NC_000913 | 839628 = | 56 (0.620) | coding (1904/2283 nt) | fiu | putative iron siderophore outer membrane transporter | |||||
| * | ? | NC_000913 | 226598 = | 74 (0.790) | 4 (0.040) | 3/268 | 8.3 | 5.3% | noncoding (840/2904 nt) | rrlH | 23S ribosomal RNA |
| ? | NC_000913 | 226697 = | NA (NA) | noncoding (939/2904 nt) | rrlH | 23S ribosomal RNA | |||||
| * | ? | NC_000913 | = 3642887 | 76 (0.820) | 3 (0.030) | 3/274 | 8.4 | 3.8% | coding (246/753 nt) | rsmJ | 16S rRNA m(2)G1516 methyltransferase |
| ? | NC_000913 | 3642891 = | 76 (0.830) | coding (242/753 nt) | rsmJ | 16S rRNA m(2)G1516 methyltransferase | |||||
| * | ? | NC_000913 | = 4430410 | 78 (0.840) | 3 (0.030) | 3/276 | 8.5 | 3.3% | coding (547/1413 nt) | cycA | serine/alanine/glycine/cycloserine:H(+)symporter |
| ? | NC_000913 | = 4430517 | 97 (1.050) | coding (654/1413 nt) | cycA | serine/alanine/glycine/cycloserine:H(+)symporter | |||||
| * | ? | NC_000913 | = 2867201 | 80 (0.860) | 3 (0.030) | 3/276 | 8.5 | 3.5% | coding (351/993 nt) | rpoS | RNA polymerase, sigma S (sigma 38) factor |
| ? | NC_000913 | = 2867282 | 88 (0.950) | coding (270/993 nt) | rpoS | RNA polymerase, sigma S (sigma 38) factor | |||||