mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.33.1 revision 8505477f25b3
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Predicted mutations | |||||||
|---|---|---|---|---|---|---|---|
| evidence | seq id | position | mutation | freq | annotation | gene | description |
| RA | CP000731 | 81 | N→G | 100% | intergenic (–/‑151) | – / → repA | –/replication protein A |
| JC | CP000731 | 6,552 | +28 bp | 100% | intergenic (+1069/‑419) | cadX → / → USA300HOU_pUSA300HOUMR0010 | cadmium efflux regulator/MarR family transcriptional regulator |
| RA | CP000731 | 12,017 | C→T | 5.4% | intergenic (+180/+43) | USA300HOU_pUSA300HOUMR0014 → / ← USA300HOU_pUSA300HOUMR0015 | recombinase/hypothetical protein |
| RA | CP000731 | 25,663 | Δ1 bp | 100% | coding (316/333 nt) | USA300HOU_pUSA300HOUMR0031 → | hypothetical protein |
| RA | USA300TCH1516_ALE | 19,009 | C→T | 18.2% | S222F (TCC→TTC) | gdpP → | Cyclic‑di‑AMP phosphodiesterase GdpP |
| RA | USA300TCH1516_ALE | 39,653 | C→A | 9.3% | S494I (AGT→ATT) | pbp ← | Beta‑lactam‑inducible penicillin‑binding protein |
| RA | USA300TCH1516_ALE | 76,969 | G→A | 87.3% | intergenic (+509/‑107) | USA300HOU_RS00140 → / → USA300HOU_RS00350 | hypothetical protein/Monoacylglycerol lipase |
| RA | USA300TCH1516_ALE | 110,660 | T→A | 10.2% | I173I (ATT→ATA) | USA300HOU_RS00515 → | putative lipoprotein |
| RA | USA300TCH1516_ALE | 110,904 | G→T | 6.7% | D255Y (GAT→TAT) | USA300HOU_RS00515 → | putative lipoprotein |
| RA | USA300TCH1516_ALE | 111,512 | A→G | 37.0% | S194S (TCA→TCG) | USA300HOU_RS00520 → | putative lipoprotein |
| RA | USA300TCH1516_ALE | 111,516 | C→A | 35.9% | Q196K (CAA→AAA) | USA300HOU_RS00520 → | putative lipoprotein |
| RA | USA300TCH1516_ALE | 111,560 | T→C | 14.1% | R210R (CGT→CGC) | USA300HOU_RS00520 → | putative lipoprotein |
| RA | USA300TCH1516_ALE | 195,286 | T→A | 100% | intergenic (‑97/‑82) | USA300HOU_RS00900 ← / → USA300HOU_RS00905 | hypothetical protein/hypothetical protein |
| RA | USA300TCH1516_ALE | 396,540 | G→A | 80.4% | A208T (GCA→ACA) | efeM → | putative iron uptake system component EfeM |
| RA | USA300TCH1516_ALE | 478,502 | C→A | 7.0% | D342E (GAC→GAA) | nuoL → | NADH‑quinone oxidoreductase subunit L |
| RA | USA300TCH1516_ALE | 512,643 | A→G | 50.0% | intergenic (+711/‑6052) | recR → / → speA_2 | Recombination protein RecR/Arginine decarboxylase |
| RA | USA300TCH1516_ALE | 596,093 | T→G | 6.9% | A375A (GCT→GCG) | fusA → | Elongation factor G |
| RA | USA300TCH1516_ALE | 607,884 | G→A | 100% | R209* (CGA→TGA) | dck ← | Deoxyadenosine/deoxycytidine kinase |
| RA | USA300TCH1516_ALE | 629,681 | C→A | 89.2% | L84I (CTA→ATA) | USA300HOU_RS02990 → | 3‑hexulose‑6‑phosphate synthase |
| RA | USA300TCH1516_ALE | 631,620 | T→C | 8.0% | intergenic (+246/‑256) | gph_1 → / → proP | Phosphoglycolate phosphatase/Proline/betaine transporter |
| RA | USA300TCH1516_ALE | 631,623 | C→A | 7.7% | intergenic (+249/‑253) | gph_1 → / → proP | Phosphoglycolate phosphatase/Proline/betaine transporter |
| RA | USA300TCH1516_ALE | 631,628 | Δ1 bp | 7.8% | intergenic (+254/‑248) | gph_1 → / → proP | Phosphoglycolate phosphatase/Proline/betaine transporter |
| RA | USA300TCH1516_ALE | 631,632:1 | +T | 8.3% | intergenic (+258/‑244) | gph_1 → / → proP | Phosphoglycolate phosphatase/Proline/betaine transporter |
| RA | USA300TCH1516_ALE | 631,637 | T→G | 8.7% | intergenic (+263/‑239) | gph_1 → / → proP | Phosphoglycolate phosphatase/Proline/betaine transporter |
| RA | USA300TCH1516_ALE | 631,640 | G→A | 8.7% | intergenic (+266/‑236) | gph_1 → / → proP | Phosphoglycolate phosphatase/Proline/betaine transporter |
| RA | USA300TCH1516_ALE | 665,392 | T→G | 100% | L79* (TTA→TGA) | paiA_1 → | Spermidine/spermine N(1)‑acetyltransferase |
| RA | USA300TCH1516_ALE | 707,910 | A→G | 90.2% | intergenic (‑1/‑121) | znuC_1 ← / → ideR | High‑affinity zinc uptake system ATP‑binding protein ZnuC/Iron‑dependent repressor IdeR |
| RA | USA300TCH1516_ALE | 849,656 | G→A | 12.2% | G261D (GGT→GAT) | USA300HOU_RS04145 → | Nucleotide‑binding protein |
| RA | USA300TCH1516_ALE | 1,002,200 | T→G | 23.9% | M173R (ATG→AGG) | mecA → | Adapter protein MecA 1 |
| RA | USA300TCH1516_ALE | 1,233,504 | T→A | 87.5% | V470D (GTT→GAT) | prkC → | Serine/threonine‑protein kinase PrkC |
| RA | USA300TCH1516_ALE | 1,416,458 | A→T | 100% | I216N (ATT→AAT) | oppD_4 ← | Oligopeptide transport ATP‑binding protein OppD |
| RA | USA300TCH1516_ALE | 1,440,085 | G→T | 100% | intergenic (‑45/+126) | cspA_2 ← / ← USA300TCH1516_01338 | Cold shock protein CspA/hypothetical protein |
| RA | USA300TCH1516_ALE | 1,513,930 | A→T | 100% | L413F (TTA→TTT) | USA300HOU_RS07375 → | hypothetical protein |
| RA | USA300TCH1516_ALE | 1,646,189 | G→C | 100% | A155G (GCA→GGA) | ypdF ← | Aminopeptidase YpdF |
| RA | USA300TCH1516_ALE | 1,744,362 | G→A | 100% | H104Y (CAC→TAC) | apt ← | Adenine phosphoribosyltransferase |
| RA | USA300TCH1516_ALE | 1,761,889 | C→A | 81.3% | D388Y (GAT→TAT) | fpgS ← | Folylpolyglutamate synthase |
| RA | USA300TCH1516_ALE | 1,934,773 | T→A | 13.0% | K159* (AAA→TAA) | USA300HOU_RS09605 ← | hypothetical protein |
| RA | USA300TCH1516_ALE | 1,934,780 | A→T | 11.9% | N156K (AAT→AAA) | USA300HOU_RS09605 ← | hypothetical protein |
| RA | USA300TCH1516_ALE | 1,963,768 | C→G | 100% | V365L (GTA→CTA) | hemY ← | Protoporphyrinogen oxidase |
| RA | USA300TCH1516_ALE | 2,010,363 | C→T | 100% | C146Y (TGT→TAT) | USA300HOU_RS10125 ← | Putative multidrug export ATP‑binding/permease protein |
| RA | USA300TCH1516_ALE | 2,046,852 | G→A | 7.5% | intergenic (+60/+29) | putP → / ← USA300HOU_RS10335 | Sodium/proline symporter/hypothetical protein |
| RA | USA300TCH1516_ALE | 2,279,705 | G→A | 100% | A943V (GCA→GTA) | ebh_3 ← | Extracellular matrix‑binding protein ebh |
| RA | USA300TCH1516_ALE | 2,352,815 | G→A | 85.5% | A92V (GCA→GTA) | rpsI ← | 30S ribosomal protein S9 |
| RA | USA300TCH1516_ALE | 2,372,419 | C→T | 11.1% | intergenic (+170/+22) | USA300TCH1516_02262 → / ← pbuG | hypothetical protein/Guanine/hypoxanthine permease PbuG |
| RA | USA300TCH1516_ALE | 2,430,691:1 | +A | 8.2% | intergenic (‑115/‑270) | suhB_2 ← / → birA_2 | Inositol‑1‑monophosphatase/Bifunctional ligase/repressor BirA |
| RA | USA300TCH1516_ALE | 2,454,626 | A→T | 100% | L48L (CTA→CTT) | lyrA → | Lysostaphin resistance protein A |
| RA | USA300TCH1516_ALE | 2,455,699 | A→T | 12.7% | H406L (CAT→CTT) | lyrA → | Lysostaphin resistance protein A |
| RA | USA300TCH1516_ALE | 2,509,782 | T→A | 10.2% | intergenic (‑94/‑276) | narT ← / → USA300HOU_RS12920 | putative nitrate transporter NarT/hypothetical protein |
| RA | USA300TCH1516_ALE | 2,509,785 | T→A | 10.2% | intergenic (‑97/‑273) | narT ← / → USA300HOU_RS12920 | putative nitrate transporter NarT/hypothetical protein |
| RA | USA300TCH1516_ALE | 2,509,792 | A→G | 10.2% | intergenic (‑104/‑266) | narT ← / → USA300HOU_RS12920 | putative nitrate transporter NarT/hypothetical protein |
| RA | USA300TCH1516_ALE | 2,532,298 | A→T | 100% | T15T (ACA→ACT) | femA_3 → | Aminoacyltransferase FemA |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | CP000731 | 34 = | 33 (0.340) | 3 (0.030) | 3/246 | NT | 7.2% | intergenic (–/‑198) | –/repA | –/replication protein A |
| ? | CP000731 | 65 = | 46 (0.500) | intergenic (–/‑167) | –/repA | –/replication protein A | |||||
| * | ? | CP000731 | 24406 = | 96 (0.990) | 5 (0.060) | 3/240 | NT | 5.7% | intergenic (+398/‑88) | USA300HOU_pUSA300HOUMR0029/USA300HOU_pUSA300HOUMR0030 | macrolide 2'‑phosphotransferase/Sin recombinase |
| ? | CP000731 | 24471 = | 77 (0.860) | intergenic (+463/‑23) | USA300HOU_pUSA300HOUMR0029/USA300HOU_pUSA300HOUMR0030 | macrolide 2'‑phosphotransferase/Sin recombinase | |||||
| * | ? | USA300TCH1516_ALE | 37094 = | 58 (1.260) | 5 (0.120) | 4/240 | NT | 9.0% | intergenic (+118/‑719) | USA300HOU_RS14915/ugpQ_1 | hypothetical protein/Glycerophosphodiester phosphodiesterase, cytoplasmic |
| ? | USA300TCH1516_ALE | 37188 = | 47 (1.100) | intergenic (+212/‑625) | USA300HOU_RS14915/ugpQ_1 | hypothetical protein/Glycerophosphodiester phosphodiesterase, cytoplasmic | |||||
| * | ? | USA300TCH1516_ALE | = 289526 | 53 (1.150) | 3 (0.070) | 3/244 | NT | 5.4% | coding (186/468 nt) | gatA_1 | PTS system galactitol‑specific EIIA component |
| ? | USA300TCH1516_ALE | = 289549 | 55 (1.270) | coding (209/468 nt) | gatA_1 | PTS system galactitol‑specific EIIA component | |||||
| * | ? | USA300TCH1516_ALE | = 329211 | 46 (1.000) | 3 (0.070) | 3/240 | NT | 6.6% | intergenic (+79/+64) | USA300HOU_RS01475/ssaA2_1 | hypothetical protein/Staphylococcal secretory antigen ssaA2 |
| ? | USA300TCH1516_ALE | = 329244 | 43 (1.010) | intergenic (+112/+31) | USA300HOU_RS01475/ssaA2_1 | hypothetical protein/Staphylococcal secretory antigen ssaA2 | |||||
| * | ? | USA300TCH1516_ALE | = 368778 | 52 (1.130) | 3 (0.070) | 3/250 | NT | 6.4% | intergenic (+212/+66) | bglK/ybbH_2 | Beta‑glucoside kinase/putative HTH‑type transcriptional regulator YbbH |
| ? | USA300TCH1516_ALE | = 368819 | 38 (0.860) | intergenic (+253/+25) | bglK/ybbH_2 | Beta‑glucoside kinase/putative HTH‑type transcriptional regulator YbbH | |||||
| * | ? | USA300TCH1516_ALE | 511377 = | 48 (1.040) | 3 (0.070) | 3/246 | NT | 6.1% | coding (42/597 nt) | recR | Recombination protein RecR |
| ? | USA300TCH1516_ALE | 511430 = | 47 (1.080) | coding (95/597 nt) | recR | Recombination protein RecR | |||||
| * | ? | USA300TCH1516_ALE | 512620 = | 47 (1.020) | 44 (1.380) +40 bp |
35/180 | NT | 57.5% | intergenic (+688/‑6075) | recR/speA_2 | Recombination protein RecR/Arginine decarboxylase |
| ? | USA300TCH1516_ALE | 1998278 = | NA (NA) | intergenic (‑6/+3329) | USA300TCH1516_01882/USA300TCH1516_01883 | tRNA‑Val/tRNA‑Ala | |||||
| * | ? | USA300TCH1516_ALE | = 517196 | NA (NA) | 5 (0.110) | 5/248 | NT | NA | intergenic (+5264/‑1499) | recR/speA_2 | Recombination protein RecR/Arginine decarboxylase |
| ? | USA300TCH1516_ALE | = 517213 | NA (NA) | intergenic (+5281/‑1482) | recR/speA_2 | Recombination protein RecR/Arginine decarboxylase | |||||
| * | ? | USA300TCH1516_ALE | 729254 = | 47 (1.020) | 3 (0.070) | 3/236 | NT | 6.8% | intergenic (+55/‑96) | USA300HOU_RS03535/aes | hypothetical protein/Acetyl esterase |
| ? | USA300TCH1516_ALE | 729295 = | 40 (0.950) | intergenic (+96/‑55) | USA300HOU_RS03535/aes | hypothetical protein/Acetyl esterase | |||||
| * | ? | USA300TCH1516_ALE | = 800994 | 50 (1.080) | 5 (0.110) | 4/246 | NT | 10.0% | intergenic (+128/‑223) | hisC_1/USA300HOU_RS03915 | Histidinol‑phosphate aminotransferase/Putative 5'(3')‑deoxyribonucleotidase |
| ? | USA300TCH1516_ALE | = 801032 | 43 (0.980) | intergenic (+166/‑185) | hisC_1/USA300HOU_RS03915 | Histidinol‑phosphate aminotransferase/Putative 5'(3')‑deoxyribonucleotidase | |||||
| * | ? | USA300TCH1516_ALE | = 891804 | 45 (0.970) | 4 (0.090) | 3/250 | NT | 8.9% | intergenic (+222/‑517) | USA300HOU_RS04385/rnmV_2 | hypothetical protein/Ribonuclease M5 |
| ? | USA300TCH1516_ALE | = 2031829 | 39 (0.880) | intergenic (+295/+195) | USA300HOU_RS10250/USA300HOU_RS10255 | hypothetical protein/hypothetical protein | |||||
| * | ? | USA300TCH1516_ALE | 1373632 = | 46 (1.000) | 3 (0.070) | 3/238 | NT | 6.9% | intergenic (+7/‑117) | USA300TCH1516_01283/sbcD | hypothetical protein/Nuclease SbcCD subunit D |
| ? | USA300TCH1516_ALE | 1373681 = | 39 (0.920) | intergenic (+56/‑68) | USA300TCH1516_01283/sbcD | hypothetical protein/Nuclease SbcCD subunit D | |||||
| * | ? | USA300TCH1516_ALE | = 1373642 | 45 (0.970) | 3 (0.070) | 3/238 | NT | 7.0% | intergenic (+17/‑107) | USA300TCH1516_01283/sbcD | hypothetical protein/Nuclease SbcCD subunit D |
| ? | USA300TCH1516_ALE | = 1373669 | 39 (0.920) | intergenic (+44/‑80) | USA300TCH1516_01283/sbcD | hypothetical protein/Nuclease SbcCD subunit D | |||||
| * | ? | USA300TCH1516_ALE | = 1623544 | 27 (0.580) | 4 (0.090) | 3/238 | NT | 13.4% | intergenic (+29/+54) | marA/malL | Multiple antibiotic resistance protein MarA/Oligo‑1,6‑glucosidase |
| ? | USA300TCH1516_ALE | = 1623575 | 27 (0.640) | intergenic (+60/+23) | marA/malL | Multiple antibiotic resistance protein MarA/Oligo‑1,6‑glucosidase | |||||
| * | ? | USA300TCH1516_ALE | = 1660030 | 40 (0.870) | 5 (0.120) | 4/238 | NT | 11.7% | coding (1279/1464 nt) | gluP | Rhomboid protease GluP |
| ? | USA300TCH1516_ALE | = 1660054 | 39 (0.920) | coding (1255/1464 nt) | gluP | Rhomboid protease GluP | |||||
| * | ? | USA300TCH1516_ALE | = 1735361 | 41 (0.890) | 4 (0.100) | 4/234 | NT | 9.8% | intergenic (+61/+100) | USA300TCH1516_01624/tcdA | putative AAA domain‑containing protein/tRNA threonylcarbamoyladenosine dehydratase |
| ? | USA300TCH1516_ALE | = 1735390 | 37 (0.890) | intergenic (+90/+71) | USA300TCH1516_01624/tcdA | putative AAA domain‑containing protein/tRNA threonylcarbamoyladenosine dehydratase | |||||
| * | ? | USA300TCH1516_ALE | 1789630 = | 44 (0.950) | 6 (0.140) | 6/238 | NT | 13.9% | intergenic (‑111/+59) | gapA2/coaE | Glyceraldehyde‑3‑phosphate dehydrogenase 2/Dephospho‑CoA kinase |
| ? | USA300TCH1516_ALE | 1789673 = | 34 (0.800) | intergenic (‑154/+16) | gapA2/coaE | Glyceraldehyde‑3‑phosphate dehydrogenase 2/Dephospho‑CoA kinase | |||||
| * | ? | USA300TCH1516_ALE | 2008942 = | 40 (0.870) | 3 (0.070) | 3/232 | NT | 8.3% | intergenic (+70/+121) | USA300HOU_RS10115/USA300HOU_RS10125 | hypothetical protein/Putative multidrug export ATP‑binding/permease protein |
| ? | USA300TCH1516_ALE | 2008991 = | 31 (0.750) | intergenic (+119/+72) | USA300HOU_RS10115/USA300HOU_RS10125 | hypothetical protein/Putative multidrug export ATP‑binding/permease protein | |||||
| * | ? | USA300TCH1516_ALE | 2080726 = | 47 (1.020) | 4 (0.100) | 4/234 | NT | 9.0% | intergenic (‑194/‑347) | USA300HOU_RS10505/aspC | hypothetical protein/Aspartate aminotransferase |
| ? | USA300TCH1516_ALE | 2080759 = | 39 (0.940) | intergenic (‑227/‑314) | USA300HOU_RS10505/aspC | hypothetical protein/Aspartate aminotransferase | |||||
| * | ? | USA300TCH1516_ALE | 2088022 = | 38 (0.820) | 3 (0.070) | 3/226 | NT | 8.8% | intergenic (+39/+56) | chp/USA300HOU_RS10560 | Chemotaxis inhibitory protein/Glycyl‑glycine endopeptidase ALE‑1 |
| ? | USA300TCH1516_ALE | 2088070 = | 29 (0.720) | intergenic (+87/+8) | chp/USA300HOU_RS10560 | Chemotaxis inhibitory protein/Glycyl‑glycine endopeptidase ALE‑1 | |||||
| * | ? | USA300TCH1516_ALE | 2207748 = | 59 (1.280) | 3 (0.070) | 3/238 | NT | 5.6% | intergenic (+109/+155) | rodA/USA300HOU_RS11255 | Peptidoglycan glycosyltransferase RodA/hypothetical protein |
| ? | USA300TCH1516_ALE | 2207798 = | 47 (1.110) | intergenic (+159/+105) | rodA/USA300HOU_RS11255 | Peptidoglycan glycosyltransferase RodA/hypothetical protein | |||||
| * | ? | USA300TCH1516_ALE | 2278438 = | 42 (0.910) | 3 (0.070) | 3/238 | NT | 6.9% | intergenic (+106/+213) | mtlD/ebh_3 | Mannitol‑1‑phosphate 5‑dehydrogenase/Extracellular matrix‑binding protein ebh |
| ? | USA300TCH1516_ALE | 2278497 = | 43 (1.020) | intergenic (+165/+154) | mtlD/ebh_3 | Mannitol‑1‑phosphate 5‑dehydrogenase/Extracellular matrix‑binding protein ebh | |||||
| * | ? | USA300TCH1516_ALE | 2303981 = | 36 (0.780) | 3 (0.070) | 3/246 | NT | 8.4% | coding (1158/1188 nt) | USA300HOU_RS11755 | putative uridylyltransferase |
| ? | USA300TCH1516_ALE | 2303997 = | 31 (0.710) | coding (1142/1188 nt) | USA300HOU_RS11755 | putative uridylyltransferase | |||||
| * | ? | USA300TCH1516_ALE | = 2609406 | 53 (1.150) | 3 (0.070) | 3/236 | NT | 5.4% | intergenic (‑236/+325) | USA300HOU_RS13450/USA300HOU_RS13455 | hypothetical protein/putative lipoprotein |
| ? | USA300TCH1516_ALE | = 2609438 | 57 (1.360) | intergenic (‑268/+293) | USA300HOU_RS13450/USA300HOU_RS13455 | hypothetical protein/putative lipoprotein | |||||
| * | ? | USA300TCH1516_ALE | = 2679966 | 46 (1.000) | 4 (0.100) | 3/230 | NT | 8.8% | intergenic (+18/+742) | ssaA2_4/USA300HOU_RS13810 | Staphylococcal secretory antigen ssaA2/hypothetical protein |
| ? | USA300TCH1516_ALE | = 2681449 | 42 (1.030) | intergenic (‑484/+95) | USA300HOU_RS13810/mvaA | hypothetical protein/3‑hydroxy‑3‑methylglutaryl‑coenzyme A reductase | |||||
| * | ? | USA300TCH1516_ALE | = 2713224 | 51 (1.100) | 3 (0.070) | 3/242 | NT | 5.6% | intergenic (‑322/+286) | isaA/USA300HOU_RS13945 | putative transglycosylase IsaA/hypothetical protein |
| ? | USA300TCH1516_ALE | = 2713244 | 53 (1.230) | intergenic (‑342/+266) | isaA/USA300HOU_RS13945 | putative transglycosylase IsaA/hypothetical protein | |||||
| * | ? | USA300TCH1516_ALE | = 2746384 | 46 (1.000) | 4 (0.090) | 4/244 | NT | 8.2% | intergenic (‑632/+53) | mqo2/acsA_2 | putative malate:quinone oxidoreductase 2/Acetyl‑coenzyme A synthetase |
| ? | USA300TCH1516_ALE | = 2746433 | 46 (1.060) | intergenic (‑681/+4) | mqo2/acsA_2 | putative malate:quinone oxidoreductase 2/Acetyl‑coenzyme A synthetase | |||||