mutation predictions | marginal predictions | summary statistics | genome diff | command line log
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breseq version 0.33.1 revision 8505477f25b3
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Marginal read alignment evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | USA300TCH1516_ALE | 512,643 | 0 | A | G | 50.7% | ‑5.6 / inf | 284 | intergenic (+711/‑6052) | recR/speA_2 | Recombination protein RecR/Arginine decarboxylase |
| * | USA300TCH1516_ALE | 111,512 | 0 | A | G | 27.8% | 279.7 / 123.4 | 170 | S194S (TCA→TCG) | USA300HOU_RS00520 | putative lipoprotein |
| * | USA300TCH1516_ALE | 111,516 | 0 | C | A | 27.3% | 332.6 / 121.1 | 165 | Q196K (CAA→AAA) | USA300HOU_RS00520 | putative lipoprotein |
| Marginal new junction evidence (lowest skew 10 of 31 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | USA300TCH1516_ALE | 2504852 = | 174 (1.380) | 65 (0.640) | 28/222 | 6.3 | 31.2% | intergenic (+156/+248) | USA300HOU_RS12890/gltT | hypothetical protein/Proton/sodium‑glutamate symport protein |
| ? | USA300TCH1516_ALE | = 2505034 | 147 (1.440) | intergenic (+338/+66) | USA300HOU_RS12890/gltT | hypothetical protein/Proton/sodium‑glutamate symport protein | |||||
| * | ? | USA300TCH1516_ALE | = 14186 | 120 (0.950) | 9 (0.080) | 7/258 | 18.2 | 7.3% | intergenic (+87/‑563) | serS_1/ygaZ | Serine‑‑tRNA ligase/Inner membrane protein YgaZ |
| ? | USA300TCH1516_ALE | = 14200 | 115 (0.970) | intergenic (+101/‑549) | serS_1/ygaZ | Serine‑‑tRNA ligase/Inner membrane protein YgaZ | |||||
| * | ? | USA300TCH1516_ALE | 1040357 = | 115 (0.910) | 7 (0.060) | 5/248 | 19.3 | 6.0% | intergenic (+18/+70) | USA300TCH1516_00966/USA300TCH1516_00967 | putative ABC transporter ATP‑binding protein/hypothetical protein |
| ? | USA300TCH1516_ALE | 1040412 = | 117 (1.030) | intergenic (+73/+15) | USA300TCH1516_00966/USA300TCH1516_00967 | putative ABC transporter ATP‑binding protein/hypothetical protein | |||||
| * | ? | USA300TCH1516_ALE | = 1292499 | 130 (1.030) | 4 (0.040) | 4/244 | 20.0 | 3.4% | intergenic (+53/‑333) | infB/rbfA | Translation initiation factor IF‑2/Ribosome‑binding factor A |
| ? | USA300TCH1516_ALE | = 1292522 | 113 (1.010) | intergenic (+76/‑310) | infB/rbfA | Translation initiation factor IF‑2/Ribosome‑binding factor A | |||||
| * | ? | USA300TCH1516_ALE | 691779 = | 151 (1.190) | 4 (0.040) | 4/248 | 20.2 | 2.8% | coding (43/1056 nt) | USA300HOU_RS03335 | hypothetical protein |
| ? | USA300TCH1516_ALE | 691838 = | 142 (1.250) | intergenic (‑17/+44) | USA300HOU_RS03335/USA300HOU_RS03340 | hypothetical protein/hypothetical protein | |||||
| * | ? | USA300TCH1516_ALE | = 2201286 | 129 (1.020) | 4 (0.030) | 4/252 | 20.4 | 3.4% | intergenic (+16/+353) | kdpE/cshA | KDP operon transcriptional regulatory protein KdpE/DEAD‑box ATP‑dependent RNA helicase CshA |
| ? | USA300TCH1516_ALE | = 2201313 | 108 (0.940) | intergenic (+43/+326) | kdpE/cshA | KDP operon transcriptional regulatory protein KdpE/DEAD‑box ATP‑dependent RNA helicase CshA | |||||
| * | ? | USA300TCH1516_ALE | = 811180 | 125 (0.990) | 4 (0.030) | 4/252 | 20.4 | 3.5% | intergenic (+22/‑644) | nrdF/fecD_1 | Ribonucleoside‑diphosphate reductase subunit beta/Fe(3+) dicitrate transport system permease protein FecD |
| ? | USA300TCH1516_ALE | = 811226 | 108 (0.940) | intergenic (+68/‑598) | nrdF/fecD_1 | Ribonucleoside‑diphosphate reductase subunit beta/Fe(3+) dicitrate transport system permease protein FecD | |||||
| * | ? | USA300TCH1516_ALE | = 365040 | 140 (1.110) | 6 (0.050) | 4/252 | 20.4 | 4.3% | intergenic (+50/+55) | nupC_1/sglT | Nucleoside permease NupC/Sodium/glucose cotransporter |
| ? | USA300TCH1516_ALE | = 365070 | 138 (1.190) | intergenic (+80/+25) | nupC_1/sglT | Nucleoside permease NupC/Sodium/glucose cotransporter | |||||
| * | ? | USA300TCH1516_ALE | 1980867 = | 101 (0.800) | 4 (0.030) | 4/256 | 20.7 | 3.9% | intergenic (‑109/+70) | USA300HOU_RS09865/USA300HOU_RS09870 | hypothetical protein/hypothetical protein |
| ? | USA300TCH1516_ALE | 1980913 = | 103 (0.880) | intergenic (‑155/+24) | USA300HOU_RS09865/USA300HOU_RS09870 | hypothetical protein/hypothetical protein | |||||
| * | ? | USA300TCH1516_ALE | 2337578 = | 140 (1.110) | 4 (0.030) | 4/258 | 20.8 | 3.2% | coding (257/417 nt) | adhR | HTH‑type transcriptional regulator AdhR |
| ? | USA300TCH1516_ALE | 2337684 = | 113 (0.960) | coding (151/417 nt) | adhR | HTH‑type transcriptional regulator AdhR | |||||