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 |
| Predicted mutations | ||||||
|---|---|---|---|---|---|---|
| evidence | seq id | position | mutation | annotation | gene | description |
| RA | USA300TCH1516_ALE | 39,378 | C→A | D586Y (GAT→TAT) | pbp ← | Beta‑lactam‑inducible penicillin‑binding protein |
| RA | USA300TCH1516_ALE | 367,644 | G→T | intergenic (‑96/‑62) | nanA ← / → bglK | N‑acetylneuraminate lyase/Beta‑glucoside kinase |
| RA | USA300TCH1516_ALE | 463,014 | C→A | E47* (GAA→TAA) | USA300HOU_RS02190 ← | hypothetical protein |
| RA | USA300TCH1516_ALE | 469,786 | A→G | G118G (GGA→GGG) | lpl2_6 → | putative lipoprotein |
| RA | USA300TCH1516_ALE | 479,553 | G→A | A194T (GCA→ACA) | USA300HOU_RS02280 → | hypothetical protein |
| RA | USA300TCH1516_ALE | 638,614 | G→T | T14K (ACA→AAA) | pdxK ← | Pyridoxine kinase |
| RA | USA300TCH1516_ALE | 707,879 | A→T | L11I (TTA→ATA) | znuC_1 ← | High‑affinity zinc uptake system ATP‑binding protein ZnuC |
| RA | USA300TCH1516_ALE | 790,778 | G→A | intergenic (+277/‑197) | kipA_1 → / → ltaS | KipI antagonist/Lipoteichoic acid synthase |
| RA | USA300TCH1516_ALE | 1,232,465 | G→C | A124P (GCG→CCG) | prkC → | Serine/threonine‑protein kinase PrkC |
| RA | USA300TCH1516_ALE | 1,416,458 | A→T | I216N (ATT→AAT) | oppD_4 ← | Oligopeptide transport ATP‑binding protein OppD |
| RA | USA300TCH1516_ALE | 1,440,007 | Δ1 bp | coding (34/201 nt) | cspA_2 ← | Cold shock protein CspA |
| RA | USA300TCH1516_ALE | 1,474,639 | C→G | A9129P (GCA→CCA) | ebh_1 ← | Extracellular matrix‑binding protein ebh |
| RA | USA300TCH1516_ALE | 1,481,355 | G→T | A6890E (GCA→GAA) | ebh_1 ← | Extracellular matrix‑binding protein ebh |
| RA | USA300TCH1516_ALE | 1,513,930 | A→T | L413F (TTA→TTT) | USA300HOU_RS07375 → | hypothetical protein |
| RA | USA300TCH1516_ALE | 1,646,189 | G→C | A155G (GCA→GGA) | ypdF ← | Aminopeptidase YpdF |
| RA | USA300TCH1516_ALE | 1,744,454 | C→T | G73D (GGC→GAC) | apt ← | Adenine phosphoribosyltransferase |
| RA | USA300TCH1516_ALE | 1,797,772 | G→C | R7G (CGC→GGC) | phoR ← | Alkaline phosphatase synthesis sensor protein PhoR |
| JC | USA300TCH1516_ALE | 1,909,272 | Δ48 bp | coding (79‑126/303 nt) | USA300HOU_RS09460 → | hypothetical protein |
| RA | USA300TCH1516_ALE | 2,010,363 | C→T | C146Y (TGT→TAT) | USA300HOU_RS10125 ← | Putative multidrug export ATP‑binding/permease protein |
| RA | USA300TCH1516_ALE | 2,021,817 | C→T | V139I (GTT→ATT) | USA300HOU_RS10190 ← | putative acyl‑CoA thioester hydrolase |
| RA | USA300TCH1516_ALE | 2,027,751 | C→G | V66L (GTA→CTA) | vraS ← | Sensor protein VraS |
| RA | USA300TCH1516_ALE | 2,279,705 | G→A | A943V (GCA→GTA) | ebh_3 ← | Extracellular matrix‑binding protein ebh |
| RA | USA300TCH1516_ALE | 2,289,252 | C→A | A80S (GCT→TCT) | cdaA ← | Cyclic di‑AMP synthase CdaA |
| RA | USA300TCH1516_ALE | 2,360,799 | A→G | G66G (GGT→GGC) | adk ← | Adenylate kinase |
| RA | USA300TCH1516_ALE | 2,372,863 | C→G | G305R (GGA→CGA) | pbuG ← | Guanine/hypoxanthine permease PbuG |
| RA | USA300TCH1516_ALE | 2,532,298 | A→T | T15T (ACA→ACT) | femA_3 → | Aminoacyltransferase FemA |
| RA | USA300TCH1516_ALE | 2,679,710 | G→T | G65V (GGC→GTC) | ssaA2_4 → | Staphylococcal secretory antigen ssaA2 |
| RA | USA300TCH1516_ALE | 2,709,297 | T→A | K544* (AAA→TAA) | oatA_2 ← | O‑acetyltransferase OatA |
| RA | USA300TCH1516_ALE | 2,856,087 | T→A | P80P (CCT→CCA) | rpoA_2 → | DNA‑directed RNA polymerase subunit alpha |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | CP000731 | 420 | 629 | 210 | 2 [1] | [1] 2 | repA | replication protein A |
| * | * | ÷ | CP000731 | 1274 | 1371 | 98 | 2 [1] | [1] 2 | repA/USA300HOU_pUSA300HOUMR0003 | replication protein A/hypothetical protein |
| * | * | ÷ | CP000731 | 4636 | 4689 | 54 | 2 [0] | [1] 2 | cadR | cadmium binding protein |
| * | * | ÷ | CP000731 | 6528 | 6619 | 92 | 2 [1] | [1] 2 | cadX/USA300HOU_pUSA300HOUMR0010 | cadmium efflux regulator/MarR family transcriptional regulator |
| * | * | ÷ | CP000731 | 7862 | 7885 | 24 | 2 [1] | [1] 2 | USA300HOU_pUSA300HOUMR0010/blaZ | MarR family transcriptional regulator/beta‑lactamase |
| * | * | ÷ | CP000731 | 13482 | 13564 | 83 | 2 [1] | [1] 2 | USA300HOU_pUSA300HOUMR0016/USA300HOU_pUSA300HOUMR0018 | IS257 transposase/3',5' aminoglycoside phosphotransferase |
| * | * | ÷ | CP000731 | 14401 | 14843 | 443 | 2 [1] | [1] 2 | USA300HOU_pUSA300HOUMR0018 | 3',5' aminoglycoside phosphotransferase |
| * | * | ÷ | CP000731 | 16144 | 16187 | 44 | 2 [1] | [1] 2 | USA300HOU_pUSA300HOUMR0019/USA300HOU_pUSA300HOUMR0021 | strepthothricin acetyltransferase/IS431 mec transposase |
| * | * | ÷ | CP000731 | 17363 | 17492 | 130 | 2 [1] | [1] 2 | USA300HOU_pUSA300HOUMR0023 | bacitracin ABC ATP binding cassette transporter, membrane protein |
| * | * | ÷ | CP000731 | 19406 | 19455 | 50 | 2 [1] | [1] 3 | USA300HOU_pUSA300HOUMR0024/USA300HOU_pUSA300HOUMR0027 | bacitracin ABC ATP binding cassette transporter, ABC protein/IS431mec transposase |
| * | * | ÷ | CP000731 | 20184 | 20371 | 188 | 2 [1] | [1] 2 | USA300HOU_pUSA300HOUMR0024/USA300HOU_pUSA300HOUMR0027 | bacitracin ABC ATP binding cassette transporter, ABC protein/IS431mec transposase |
| * | * | ÷ | CP000731 | 20638 | 20670 | 33 | 2 [1] | [1] 2 | USA300HOU_pUSA300HOUMR0027 | IS431mec transposase |
| * | * | ÷ | CP000731 | 21260 | 21493 | 234 | 2 [1] | [1] 2 | USA300HOU_pUSA300HOUMR0027/USA300HOU_pUSA300HOUMR0028 | IS431mec transposase/macrolide transporter |
| * | * | ÷ | CP000731 | 22008 | 22048 | 41 | 2 [1] | [1] 2 | USA300HOU_pUSA300HOUMR0028 | macrolide transporter |
| * | * | ÷ | CP000731 | 23642 | 23825 | 184 | 2 [1] | [1] 2 | USA300HOU_pUSA300HOUMR0029 | macrolide 2'‑phosphotransferase |
| * | * | ÷ | CP000731 | 25791 | 25814 | 24 | 2 [1] | [0] 2 | USA300HOU_pUSA300HOUMR0032 | possible transcriptional regulator |
| * | * | ÷ | CP000731 | 26929 | 27041 | 113 | 2 [1] | [0] NA | USA300HOU_pUSA300HOUMR0033/– | partitioning protein/– |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | USA300TCH1516_ALE | 512620 = | 137 (1.200) | 79 (0.980) +40 bp |
57/196 | 0.3 | 44.8% | 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 | |||||