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 | 111,512 | 0 | A | G | 28.8% | 547.7 / 266.7 | 337 | S194S (TCA→TCG) | USA300HOU_RS00520 | putative lipoprotein |
| * | USA300TCH1516_ALE | 111,516 | 0 | C | A | 28.1% | 653.7 / 287.7 | 320 | Q196K (CAA→AAA) | USA300HOU_RS00520 | putative lipoprotein |
| * | USA300TCH1516_ALE | 2,021,817 | 0 | C | T | 27.2% | 313.1 / 125.3 | 180 | V139I (GTT→ATT) | USA300HOU_RS10190 | putative acyl‑CoA thioester hydrolase |
| * | USA300TCH1516_ALE | 1,931,599 | 0 | A | T | 26.3% | 933.4 / inf | 487 | L1217I (TTA→ATA) | USA300HOU_RS09605 | hypothetical protein |
| * | USA300TCH1516_ALE | 2,143,110 | 0 | G | A | 24.6% | 470.4 / 163.1 | 256 | V163V (GTG→GTA) | USA300HOU_RS10935 | hypothetical protein |
| * | USA300TCH1516_ALE | 2,372,413 | 0 | C | G | 21.5% | 591.9 / 157.4 | 242 | intergenic (+164/+28) | USA300TCH1516_02262/pbuG | hypothetical protein/Guanine/hypoxanthine permease PbuG |
| Marginal new junction evidence (lowest skew 10 of 1095 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | USA300TCH1516_ALE | = 1205323 | 248 (1.180) | 353 (2.930) +38 bp |
25/104 | 5.1 | 70.7% | intergenic (‑204/‑365) | USA300HOU_RS15290/lspA | hypothetical protein/Lipoprotein signal peptidase |
| ? | USA300TCH1516_ALE | 2478252 = | 263 (1.250) | intergenic (+139/‑436) | USA300HOU_RS12760/USA300HOU_RS12765 | hypothetical protein/hypothetical protein | |||||
| * | ? | USA300TCH1516_ALE | = 1205323 | 248 (1.180) | 353 (2.930) +38 bp |
25/104 | 5.1 | 71.3% | intergenic (‑204/‑365) | USA300HOU_RS15290/lspA | hypothetical protein/Lipoprotein signal peptidase |
| ? | USA300TCH1516_ALE | = 1443739 | NA (NA) | intergenic (‑312/+41) | USA300TCH1516_01342/brnQ_3 | hypothetical protein/Branched‑chain amino acid transport system 2 carrier protein | |||||
| * | ? | USA300TCH1516_ALE | = 1205323 | 248 (1.180) | 353 (2.930) +38 bp |
25/104 | 5.1 | 72.9% | intergenic (‑204/‑365) | USA300HOU_RS15290/lspA | hypothetical protein/Lipoprotein signal peptidase |
| ? | USA300TCH1516_ALE | 1426517 = | 211 (1.000) | intergenic (‑248/+724) | pstS/cvfB | Phosphate‑binding protein PstS/Conserved virulence factor B | |||||
| * | ? | USA300TCH1516_ALE | 1181465 = | 266 (1.270) | 33 (0.170) | 20/162 | 10.9 | 12.5% | intergenic (+32/+442) | USA300HOU_RS05885/USA300TCH1516_01103 | hypothetical protein/tRNA‑Arg |
| ? | USA300TCH1516_ALE | 1181489 = | 224 (1.190) | intergenic (+56/+418) | USA300HOU_RS05885/USA300TCH1516_01103 | hypothetical protein/tRNA‑Arg | |||||
| * | ? | USA300TCH1516_ALE | = 2740979 | 194 (0.920) | 34 (0.190) | 17/152 | 11.3 | 16.7% | intergenic (+21/+60) | yhdG_2/USA300HOU_RS14115 | putative amino acid permease YhdG/Isoleucine 2‑epimerase |
| ? | USA300TCH1516_ALE | = 2741001 | 177 (1.000) | intergenic (+43/+38) | yhdG_2/USA300HOU_RS14115 | putative amino acid permease YhdG/Isoleucine 2‑epimerase | |||||
| * | ? | USA300TCH1516_ALE | 2473265 = | 198 (0.940) | 37 (0.220) | 16/146 | 11.3 | 18.5% | intergenic (+99/+131) | USA300HOU_RS12730/bcr_1 | hypothetical protein/Bicyclomycin resistance protein |
| ? | USA300TCH1516_ALE | 2473309 = | 165 (0.970) | intergenic (+143/+87) | USA300HOU_RS12730/bcr_1 | hypothetical protein/Bicyclomycin resistance protein | |||||
| * | ? | USA300TCH1516_ALE | 2256396 = | 200 (0.950) | 31 (0.180) | 17/152 | 11.3 | 15.0% | intergenic (+49/+72) | deoD1/dps | Purine nucleoside phosphorylase DeoD‑type 1/General stress protein 20U |
| ? | USA300TCH1516_ALE | 2256443 = | 182 (1.030) | intergenic (+96/+25) | deoD1/dps | Purine nucleoside phosphorylase DeoD‑type 1/General stress protein 20U | |||||
| * | ? | CP000731 | 21026 = | NA (NA) | 123 (0.230) | 20/168 | 11.3 | 46.5% | coding (45/675 nt) | USA300HOU_pUSA300HOUMR0027 | IS431mec transposase |
| ? | USA300TCH1516_ALE | = 76274 | 152 (0.720) | coding (60/246 nt) | USA300HOU_RS00140 | hypothetical protein | |||||
| * | ? | CP000731 | 21026 = | NA (NA) | 123 (0.230) | 20/168 | 11.3 | 37.2% | coding (45/675 nt) | USA300HOU_pUSA300HOUMR0027 | IS431mec transposase |
| ? | USA300TCH1516_ALE | 36492 = | 223 (1.060) | coding (60/675 nt) | USA300HOU_RS00140 | hypothetical protein | |||||
| * | ? | USA300TCH1516_ALE | 1507967 = | 257 (1.220) | 28 (0.160) | 16/148 | 11.5 | 11.7% | intergenic (‑392/+83) | ald1/ypcP | Alanine dehydrogenase 1/5'‑3' exonuclease |
| ? | USA300TCH1516_ALE | 1508010 = | 212 (1.230) | intergenic (‑435/+40) | ald1/ypcP | Alanine dehydrogenase 1/5'‑3' exonuclease | |||||