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 | USA300TCH1516_ALE | 76,969 | G→A | 21.3% | intergenic (+509/‑107) | USA300HOU_RS00140 → / → USA300HOU_RS00350 | hypothetical protein/Monoacylglycerol lipase |
| RA | USA300TCH1516_ALE | 110,660 | T→A | 6.7% | I173I (ATT→ATA) | USA300HOU_RS00515 → | putative lipoprotein |
| RA | USA300TCH1516_ALE | 111,512 | A→G | 28.3% | S194S (TCA→TCG) | USA300HOU_RS00520 → | putative lipoprotein |
| RA | USA300TCH1516_ALE | 111,516 | C→A | 27.8% | Q196K (CAA→AAA) | USA300HOU_RS00520 → | putative lipoprotein |
| RA | USA300TCH1516_ALE | 111,560 | T→C | 9.7% | R210R (CGT→CGC) | USA300HOU_RS00520 → | putative lipoprotein |
| RA | USA300TCH1516_ALE | 195,286 | T→A | 21.4% | intergenic (‑97/‑82) | USA300HOU_RS00900 ← / → USA300HOU_RS00905 | hypothetical protein/hypothetical protein |
| RA | USA300TCH1516_ALE | 340,387 | A→T | 15.3% | K19M (AAG→ATG) | esxC → | ESAT‑6 secretion system extracellular protein C |
| RA | USA300TCH1516_ALE | 382,916 | C→A | 23.0% | G331C (GGT→TGT) | ulaA ← | Ascorbate‑specific PTS system EIIC component |
| RA | USA300TCH1516_ALE | 396,540 | G→A | 11.5% | A208T (GCA→ACA) | efeM → | putative iron uptake system component EfeM |
| RA | USA300TCH1516_ALE | 478,502 | C→A | 85.6% | D342E (GAC→GAA) | nuoL → | NADH‑quinone oxidoreductase subunit L |
| RA | USA300TCH1516_ALE | 512,643 | A→G | 35.7% | intergenic (+711/‑6052) | recR → / → speA_2 | Recombination protein RecR/Arginine decarboxylase |
| RA | USA300TCH1516_ALE | 554,989 | T→C | 8.4% | A315A (GCT→GCC) | lysS → | Lysine‑‑tRNA ligase |
| RA | USA300TCH1516_ALE | 584,121 | G→T | 76.8% | intergenic (+205/‑67) | rplA → / → rplJ | 50S ribosomal protein L1/50S ribosomal protein L10 |
| RA | USA300TCH1516_ALE | 607,884 | G→A | 19.1% | R209* (CGA→TGA) | dck ← | Deoxyadenosine/deoxycytidine kinase |
| RA | USA300TCH1516_ALE | 665,392 | T→G | 18.3% | L79* (TTA→TGA) | paiA_1 → | Spermidine/spermine N(1)‑acetyltransferase |
| RA | USA300TCH1516_ALE | 707,909 | A→T | 78.4% | M1M (TTG→ATG) † | znuC_1 ← | High‑affinity zinc uptake system ATP‑binding protein ZnuC |
| RA | USA300TCH1516_ALE | 707,910 | A→G | 20.2% | intergenic (‑1/‑121) | znuC_1 ← / → ideR | High‑affinity zinc uptake system ATP‑binding protein ZnuC/Iron‑dependent repressor IdeR |
| RA | USA300TCH1516_ALE | 832,706 | A→T | 5.7% | I488F (ATT→TTT) | secA_1 → | Protein translocase subunit SecA |
| RA | USA300TCH1516_ALE | 973,213 | C→A | 100% | E175* (GAG→TAG) | yitU_1 ← | 5‑amino‑6‑(5‑phospho‑D‑ribitylamino)uracil phosphatase YitU |
| RA | USA300TCH1516_ALE | 1,002,200 | T→G | 90.9% | M173R (ATG→AGG) | mecA → | Adapter protein MecA 1 |
| RA | USA300TCH1516_ALE | 1,105,994 | T→C | 85.3% | T12T (ACT→ACC) | pdhD → | Dihydrolipoyl dehydrogenase |
| RA | USA300TCH1516_ALE | 1,196,508 | C→A | 83.8% | S338Y (TCT→TAT) | ftsZ → | Cell division protein FtsZ |
| RA | USA300TCH1516_ALE | 1,231,470 | A→C | 45.3% | M39L (ATG→CTG) | stp → | Serine/threonine phosphatase stp |
| RA | USA300TCH1516_ALE | 1,233,504 | T→A | 15.8% | V470D (GTT→GAT) | prkC → | Serine/threonine‑protein kinase PrkC |
| RA | USA300TCH1516_ALE | 1,391,351 | G→A | 26.5% | G196S (GGT→AGT) | alsT → | Amino‑acid carrier protein AlsT |
| RA | USA300TCH1516_ALE | 1,416,458 | A→T | 100% | I216N (ATT→AAT) | oppD_4 ← | Oligopeptide transport ATP‑binding protein OppD |
| RA | USA300TCH1516_ALE | 1,513,930 | A→T | 100% | L413F (TTA→TTT) | USA300HOU_RS07375 → | hypothetical protein |
| RA | USA300TCH1516_ALE | 1,539,250 | C→G | 100% | intergenic (‑349/+37) | aroC ← / ← USA300HOU_RS07505 | Chorismate synthase/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 | 19.0% | H104Y (CAC→TAC) | apt ← | Adenine phosphoribosyltransferase |
| RA | USA300TCH1516_ALE | 1,744,473 | C→T | 82.9% | A67T (GCT→ACT) | apt ← | Adenine phosphoribosyltransferase |
| RA | USA300TCH1516_ALE | 1,963,768 | C→G | 12.9% | 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 | 2,027,191 | A→C | 9.8% | H252Q (CAT→CAG) | vraS ← | Sensor protein VraS |
| RA | USA300TCH1516_ALE | 2,027,694 | A→T | 14.4% | S85T (TCA→ACA) | vraS ← | Sensor protein VraS |
| RA | USA300TCH1516_ALE | 2,162,009 | C→A | 7.6% | Q428K (CAA→AAA) | mutS_2 → | DNA mismatch repair protein MutS |
| RA | USA300TCH1516_ALE | 2,279,705 | G→A | 100% | A943V (GCA→GTA) | ebh_3 ← | Extracellular matrix‑binding protein ebh |
| RA | USA300TCH1516_ALE | 2,337,959 | C→T | 86.9% | intergenic (‑125/‑283) | adhR ← / → USA300HOU_RS11940 | HTH‑type transcriptional regulator AdhR/Hyaluronate lyase |
| RA | USA300TCH1516_ALE | 2,352,815 | G→A | 11.4% | A92V (GCA→GTA) | rpsI ← | 30S ribosomal protein S9 |
| RA | USA300TCH1516_ALE | 2,454,626 | A→T | 12.0% | L48L (CTA→CTT) | lyrA → | Lysostaphin resistance protein A |
| RA | USA300TCH1516_ALE | 2,455,692 | Δ1 bp | 69.7% | coding (1210/1260 nt) | lyrA → | Lysostaphin resistance protein A |
| RA | USA300TCH1516_ALE | 2,455,698 | C→A | 100% | H406N (CAT→AAT) ‡ | lyrA → | Lysostaphin resistance protein A |
| RA | USA300TCH1516_ALE | 2,455,699 | A→T | 76.6% | H406L (CAT→CTT) ‡ | lyrA → | Lysostaphin resistance protein A |
| RA | USA300TCH1516_ALE | 2,473,767 | T→C | 6.3% | I280V (ATA→GTA) | bcr_1 ← | Bicyclomycin resistance protein |
| RA | USA300TCH1516_ALE | 2,532,298 | A→T | 100% | T15T (ACA→ACT) | femA_3 → | Aminoacyltransferase FemA |
| RA | USA300TCH1516_ALE | 2,628,458 | G→A | 7.3% | G250G (GGC→GGT) | gtaB ← | UTP‑‑glucose‑1‑phosphate uridylyltransferase |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | CP000731 | 655 | 1009 | 355 | 2 [1] | [1] 2 | repA | replication protein A |
| * | * | ÷ | CP000731 | 1754 | 1969 | 216 | 2 [0] | [0] 2 | repA/USA300HOU_pUSA300HOUMR0003 | replication protein A/hypothetical protein |
| * | * | ÷ | CP000731 | 2111 | 2116 | 6 | 2 [0] | [1] 2 | USA300HOU_pUSA300HOUMR0003 | hypothetical protein |
| * | * | ÷ | CP000731 | 3453 | 3700 | 248 | 2 [1] | [1] 2 | USA300HOU_pUSA300HOUMR0005/USA300HOU_pUSA300HOUMR0006 | hypothetical protein/hypothetical protein |
| * | * | ÷ | CP000731 | 4615 | 4802 | 188 | 3 [1] | [1] 2 | cadR | cadmium binding protein |
| * | * | ÷ | CP000731 | 4861 | 5001 | 141 | 2 [1] | [1] 2 | cadR | cadmium binding protein |
| * | * | ÷ | CP000731 | 5143 | 5193 | 51 | 2 [1] | [1] 4 | cadX | cadmium efflux regulator |
| * | * | ÷ | CP000731 | 6467 | 6611 | 145 | 2 [1] | [1] 2 | cadX/USA300HOU_pUSA300HOUMR0010 | cadmium efflux regulator/MarR family transcriptional regulator |
| * | * | ÷ | CP000731 | 8188 | 8329 | 142 | 2 [1] | [1] 2 | blaZ | beta‑lactamase |
| * | * | ÷ | CP000731 | 8367 | 8538 | 172 | 2 [1] | [1] 2 | blaZ | beta‑lactamase |
| * | * | ÷ | CP000731 | 9236 | 9269 | 34 | 2 [1] | [1] 2 | blaR | beta‑lactamase regulator BlaR |
| * | * | ÷ | CP000731 | 10913 | 11342 | 430 | 3 [1] | [1] 2 | [blaI]–[USA300HOU_pUSA300HOUMR0014] | [blaI],[USA300HOU_pUSA300HOUMR0014] |
| * | * | ÷ | CP000731 | 15046 | 15223 | 178 | 2 [1] | [1] 2 | [USA300HOU_pUSA300HOUMR0019] | [USA300HOU_pUSA300HOUMR0019] |
| * | * | ÷ | CP000731 | 15881 | 16002 | 122 | 2 [1] | [1] 2 | USA300HOU_pUSA300HOUMR0019/USA300HOU_pUSA300HOUMR0021 | strepthothricin acetyltransferase/IS431 mec transposase |
| * | * | ÷ | CP000731 | 18124 | 18162 | 39 | 2 [1] | [1] 2 | USA300HOU_pUSA300HOUMR0024 | bacitracin ABC ATP binding cassette transporter, ABC protein |
| * | * | ÷ | CP000731 | 24716 | 24953 | 238 | 2 [1] | [0] 2 | USA300HOU_pUSA300HOUMR0030 | Sin recombinase |
| * | * | ÷ | CP000731 | 26238 | 26710 | 473 | 2 [1] | [1] 2 | USA300HOU_pUSA300HOUMR0033 | partitioning protein |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | USA300TCH1516_ALE | 512620 = | 56 (1.080) | 31 (0.870) +40 bp |
26/180 | NT | 44.5% | 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 | = 907281 | 45 (0.870) | 4 (0.080) | 3/240 | NT | 8.6% | intergenic (+390/‑39) | USA300HOU_RS04490/USA300HOU_RS04495 | hypothetical protein/hypothetical protein |
| ? | USA300TCH1516_ALE | = 907290 | 44 (0.920) | intergenic (+399/‑30) | USA300HOU_RS04490/USA300HOU_RS04495 | hypothetical protein/hypothetical protein | |||||
| * | ? | USA300TCH1516_ALE | 1030884 = | 55 (1.060) | 3 (0.060) | 3/234 | NT | 5.9% | intergenic (+7/‑129) | ktrB_1/yfkN_2 | Ktr system potassium uptake protein B/Trifunctional nucleotide phosphoesterase protein YfkN |
| ? | USA300TCH1516_ALE | 1030933 = | 47 (1.010) | intergenic (+56/‑80) | ktrB_1/yfkN_2 | Ktr system potassium uptake protein B/Trifunctional nucleotide phosphoesterase protein YfkN | |||||
| * | ? | USA300TCH1516_ALE | = 2442821 | 45 (0.870) | 5 (0.110) | 5/228 | NT | 11.6% | intergenic (+18/+40) | glvR/USA300HOU_RS12585 | HTH‑type transcriptional regulator GlvR/hypothetical protein |
| ? | USA300TCH1516_ALE | = 2442838 | 37 (0.810) | intergenic (+35/+23) | glvR/USA300HOU_RS12585 | HTH‑type transcriptional regulator GlvR/hypothetical protein | |||||
| * | ? | USA300TCH1516_ALE | 2561201 = | 54 (1.040) | 3 (0.060) | 3/232 | NT | 6.0% | intergenic (+30/+33) | USA300HOU_RS13195/cpdA | hypothetical protein/3',5'‑cyclic adenosine monophosphate phosphodiesterase CpdA |
| ? | USA300TCH1516_ALE | 2561237 = | 46 (0.990) | coding (804/807 nt) | cpdA | 3',5'‑cyclic adenosine monophosphate phosphodiesterase CpdA | |||||