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 |
| MC | CP000731 | 1 | Δ27,041 bp | 100% | repA–USA300HOU_pUSA300HOUMR0033 | 26 genes repA, USA300HOU_pUSA300HOUMR0003, USA300HOU_pUSA300HOUMR0004, USA300HOU_pUSA300HOUMR0005, USA300HOU_pUSA300HOUMR0006, cadR, cadX, USA300HOU_pUSA300HOUMR0010, blaZ, blaR, blaI, USA300HOU_pUSA300HOUMR0014, USA300HOU_pUSA300HOUMR0015, USA300HOU_pUSA300HOUMR0016, USA300HOU_pUSA300HOUMR0018, USA300HOU_pUSA300HOUMR0019, USA300HOU_pUSA300HOUMR0021, USA300HOU_pUSA300HOUMR0023, USA300HOU_pUSA300HOUMR0024, USA300HOU_pUSA300HOUMR0027, USA300HOU_pUSA300HOUMR0028, USA300HOU_pUSA300HOUMR0029, USA300HOU_pUSA300HOUMR0030, USA300HOU_pUSA300HOUMR0031, USA300HOU_pUSA300HOUMR0032, USA300HOU_pUSA300HOUMR0033 |
|
| RA | USA300TCH1516_ALE | 39,672 | C→A | 100% | V488F (GTT→TTT) | pbp ← | Beta‑lactam‑inducible penicillin‑binding protein |
| RA | USA300TCH1516_ALE | 76,969 | G→A | 100% | intergenic (+509/‑107) | USA300HOU_RS00140 → / → USA300HOU_RS00350 | hypothetical protein/Monoacylglycerol lipase |
| RA | USA300TCH1516_ALE | 110,660 | T→A | 18.0% | I173I (ATT→ATA) | USA300HOU_RS00515 → | putative lipoprotein |
| RA | USA300TCH1516_ALE | 111,512 | A→G | 35.5% | S194S (TCA→TCG) | USA300HOU_RS00520 → | putative lipoprotein |
| RA | USA300TCH1516_ALE | 111,516 | C→A | 33.7% | Q196K (CAA→AAA) | 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 | 100% | A208T (GCA→ACA) | efeM → | putative iron uptake system component EfeM |
| RA | USA300TCH1516_ALE | 459,019 | G→A | 7.7% | G27E (GGG→GAG) | USA300HOU_RS02175 → | hypothetical protein |
| RA | USA300TCH1516_ALE | 512,643 | A→G | 42.8% | intergenic (+711/‑6052) | recR → / → speA_2 | Recombination protein RecR/Arginine decarboxylase |
| RA | USA300TCH1516_ALE | 607,884 | G→A | 100% | R209* (CGA→TGA) | dck ← | Deoxyadenosine/deoxycytidine kinase |
| RA | USA300TCH1516_ALE | 629,681 | C→A | 100% | L84I (CTA→ATA) | USA300HOU_RS02990 → | 3‑hexulose‑6‑phosphate synthase |
| 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 | 100% | intergenic (‑1/‑121) | znuC_1 ← / → ideR | High‑affinity zinc uptake system ATP‑binding protein ZnuC/Iron‑dependent repressor IdeR |
| RA | USA300TCH1516_ALE | 745,728 | A→G | 17.4% | K9E (AAA→GAA) | USA300HOU_RS03615 → | putative transcriptional regulatory protein |
| RA | USA300TCH1516_ALE | 804,673 | A→T | 100% | L135I (TTA→ATA) | dtpT ← | Di‑/tripeptide transporter |
| RA | USA300TCH1516_ALE | 933,033 | T→C | 100% | intergenic (‑74/‑27) | nfuA ← / → USA300HOU_RS04645 | Fe/S biogenesis protein NfuA/hypothetical protein |
| RA | USA300TCH1516_ALE | 1,064,444 | Δ1 bp | 100% | coding (45/1218 nt) | ywtF ← | Putative transcriptional regulator YwtF |
| RA | USA300TCH1516_ALE | 1,233,504 | T→A | 100% | 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 | 1,430,220 | T→C | 10.5% | intergenic (+329/‑531) | ybiT → / → lysC | putative ABC transporter ATP‑binding protein YbiT/Aspartokinase |
| 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 | 1,633,076 | C→T | 6.8% | E75K (GAA→AAA) | pdhC_2 ← | Dihydrolipoyllysine‑residue acetyltransferase component of pyruvate dehydrogenase complex |
| 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 |
| MC JC | USA300TCH1516_ALE | 1,747,374 | Δ3 bp | 100% | coding (2073‑2075/2280 nt) | USA300HOU_RS08710 ← | Heme uptake protein MmpL11 |
| RA | USA300TCH1516_ALE | 1,761,889 | C→A | 100% | D388Y (GAT→TAT) | fpgS ← | Folylpolyglutamate synthase |
| 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 | 2,028,583 | G→T | 100% | A21D (GCC→GAC) | USA300HOU_RS10230 ← | hypothetical protein |
| RA | USA300TCH1516_ALE | 2,223,916 | A→T | 6.2% | L420* (TTA→TAA) | atpA ← | ATP synthase subunit alpha |
| RA | USA300TCH1516_ALE | 2,279,705 | G→A | 100% | A943V (GCA→GTA) | ebh_3 ← | Extracellular matrix‑binding protein ebh |
| RA | USA300TCH1516_ALE | 2,289,257 | A→C | 66.6% | V78G (GTA→GGA) | cdaA ← | Cyclic di‑AMP synthase CdaA |
| RA | USA300TCH1516_ALE | 2,352,815 | G→A | 100% | A92V (GCA→GTA) | rpsI ← | 30S ribosomal protein S9 |
| RA | USA300TCH1516_ALE | 2,454,626 | A→T | 100% | L48L (CTA→CTT) | lyrA → | Lysostaphin resistance protein A |
| RA | USA300TCH1516_ALE | 2,480,567 | C→T | 8.6% | R113H (CGC→CAC) | USA300HOU_RS12775 ← | putative ABC transporter permease |
| MC JC | USA300TCH1516_ALE | 2,501,188 | Δ3,014 bp | 100% | melR_2–ydaG | melR_2, ydaG | |
| RA | USA300TCH1516_ALE | 2,530,133 | T→A | 11.5% | intergenic (‑196/+99) | zinT ← / ← yoeB | Metal‑binding protein ZinT/Toxin YoeB |
| RA | USA300TCH1516_ALE | 2,532,298 | A→T | 100% | T15T (ACA→ACT) | femA_3 → | Aminoacyltransferase FemA |
| RA | USA300TCH1516_ALE | 2,709,609 | C→A | 18.6% | E440* (GAG→TAG) | oatA_2 ← | O‑acetyltransferase OatA |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | USA300TCH1516_ALE | 512620 = | 48 (1.060) | 26 (0.830) +40 bp |
19/178 | NT | 44.1% | 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 | 2660570 = | 42 (0.920) | 4 (0.100) | 4/234 | NT | 10.1% | intergenic (+12/+237) | ldhD_1/ybiV | D‑lactate dehydrogenase/Sugar phosphatase YbiV |
| ? | USA300TCH1516_ALE | 2660603 = | 33 (0.800) | intergenic (+45/+204) | ldhD_1/ybiV | D‑lactate dehydrogenase/Sugar phosphatase YbiV | |||||