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 | CP000731 | 81 | N→G | intergenic (–/‑151) | – / → repA | –/replication protein A |
| JC | CP000731 | 6,552 | +28 bp | intergenic (+1069/‑419) | cadX → / → USA300HOU_pUSA300HOUMR0010 | cadmium efflux regulator/MarR family transcriptional regulator |
| RA | CP000731 | 8,740 | T→C | I8V (ATT→GTT) | blaZ ← | beta‑lactamase |
| RA | CP000731 | 25,669 | (A)7→6 | coding (322/333 nt) | USA300HOU_pUSA300HOUMR0031 → | hypothetical protein |
| RA | USA300TCH1516_ALE | 39,195 | T→C | K647E (AAA→GAA) | pbp ← | Beta‑lactam‑inducible penicillin‑binding protein |
| RA | USA300TCH1516_ALE | 39,378 | C→T | D586N (GAT→AAT) | pbp ← | Beta‑lactam‑inducible penicillin‑binding protein |
| RA | USA300TCH1516_ALE | 51,334 | (G)7→8 | intergenic (‑132/‑7) | USA300HOU_RS00210 ← / → USA300HOU_RS00215 | hypothetical protein/hypothetical protein |
| RA | USA300TCH1516_ALE | 76,969 | G→A | intergenic (+509/‑107) | USA300HOU_RS00140 → / → USA300HOU_RS00350 | hypothetical protein/Monoacylglycerol lipase |
| RA | USA300TCH1516_ALE | 93,268 | G→A | A73T (GCT→ACT) | glpE → | Thiosulfate sulfurtransferase GlpE |
| RA | USA300TCH1516_ALE | 129,796 | G→C | intergenic (‑209/+212) | spa ← / ← sarS | Immunoglobulin G‑binding protein A/HTH‑type transcriptional regulator SarS |
| RA | USA300TCH1516_ALE | 169,407 | G→A | G82E (GGA→GAA) | repE → | Replication initiation protein |
| RA | USA300TCH1516_ALE | 195,286 | T→A | intergenic (‑97/‑82) | USA300HOU_RS00900 ← / → USA300HOU_RS00905 | hypothetical protein/hypothetical protein |
| RA | USA300TCH1516_ALE | 266,981 | A→G | P228P (CCA→CCG) | USA300HOU_RS01175 → | Staphylocoagulase |
| RA | USA300TCH1516_ALE | 396,540 | G→A | A208T (GCA→ACA) | efeM → | putative iron uptake system component EfeM |
| RA | USA300TCH1516_ALE | 505,514 | C→T | A469V (GCG→GTG) | treP_1 → | PTS system trehalose‑specific EIIBC component |
| RA | USA300TCH1516_ALE | 536,758 | C→T | P202L (CCA→CTA) | rplY → | 50S ribosomal protein L25 |
| RA | USA300TCH1516_ALE | 607,884 | G→A | R209* (CGA→TGA) | dck ← | Deoxyadenosine/deoxycytidine kinase |
| RA | USA300TCH1516_ALE | 629,681 | C→A | L84I (CTA→ATA) | USA300HOU_RS02990 → | 3‑hexulose‑6‑phosphate synthase |
| RA | USA300TCH1516_ALE | 665,392 | T→G | L79* (TTA→TGA) | paiA_1 → | Spermidine/spermine N(1)‑acetyltransferase |
| RA | USA300TCH1516_ALE | 707,910 | A→G | intergenic (‑1/‑121) | znuC_1 ← / → ideR | High‑affinity zinc uptake system ATP‑binding protein ZnuC/Iron‑dependent repressor IdeR |
| RA | USA300TCH1516_ALE | 744,375 | A→T | I506F (ATT→TTT) | melR_1 → | Melibiose operon regulatory protein |
| RA | USA300TCH1516_ALE | 749,249 | C→T | S59S (AGC→AGT) | setC → | Sugar efflux transporter C |
| RA | USA300TCH1516_ALE | 890,260 | T→C | V39A (GTT→GCT) | gcvH → | Glycine cleavage system H protein |
| RA | USA300TCH1516_ALE | 1,017,678 | T→C | F391S (TTC→TCC) | acp → | Sodium/proton‑dependent alanine carrier protein |
| RA | USA300TCH1516_ALE | 1,063,912 | +C | coding (577/1218 nt) | ywtF ← | Putative transcriptional regulator YwtF |
| RA | USA300TCH1516_ALE | 1,125,066 | G→C | E729Q (GAG→CAG) | cfiB_1 → | 2‑oxoglutarate carboxylase small subunit |
| RA | USA300TCH1516_ALE | 1,163,829 | T→C | V72A (GTG→GCG) | USA300HOU_RS05765 → | Putative metallophosphoesterase MG207 |
| RA | USA300TCH1516_ALE | 1,233,504 | T→A | V470D (GTT→GAT) | prkC → | Serine/threonine‑protein kinase PrkC |
| RA | USA300TCH1516_ALE | 1,298,108 | T→A | intergenic (+4/‑232) | pnp → / → rnj2 | Polyribonucleotide nucleotidyltransferase/Ribonuclease J 2 |
| RA | USA300TCH1516_ALE | 1,324,256 | (A)9→8 | coding (1028/2010 nt) | mutL → | DNA mismatch repair protein MutL |
| RA | USA300TCH1516_ALE | 1,358,236 | A→G | G300G (GGA→GGG) | hom → | Homoserine dehydrogenase |
| RA | USA300TCH1516_ALE | 1,416,458 | A→T | I216N (ATT→AAT) | oppD_4 ← | Oligopeptide transport ATP‑binding protein OppD |
| RA | USA300TCH1516_ALE | 1,440,085 | G→T | intergenic (‑45/+126) | cspA_2 ← / ← USA300TCH1516_01338 | Cold shock protein CspA/hypothetical protein |
| RA | USA300TCH1516_ALE | 1,499,376 | C→A | G883V (GGT→GTT) | 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 | 1,613,762 | T→C | intergenic (‑31/‑37) | scpA ← / → USA300HOU_RS08000 | Segregation and condensation protein A/hypothetical protein |
| RA | USA300TCH1516_ALE | 1,624,673 | T→A | K192I (AAA→ATA) | malL ← | Oligo‑1,6‑glucosidase |
| RA | USA300TCH1516_ALE | 1,646,189 | G→C | A155G (GCA→GGA) | ypdF ← | Aminopeptidase YpdF |
| RA | USA300TCH1516_ALE | 1,744,362 | G→A | H104Y (CAC→TAC) | apt ← | Adenine phosphoribosyltransferase |
| RA | USA300TCH1516_ALE | 1,761,889 | C→A | D388Y (GAT→TAT) | fpgS ← | Folylpolyglutamate synthase |
| RA | USA300TCH1516_ALE | 1,769,572 | A→G | V295V (GTT→GTC) | hemB ← | Delta‑aminolevulinic acid dehydratase |
| RA | USA300TCH1516_ALE | 1,830,883 | C→T | K79K (AAG→AAA) | ezrA ← | Septation ring formation regulator EzrA |
| RA | USA300TCH1516_ALE | 1,851,260 | C→A | A115S (GCG→TCG) | acsA_1 ← | Acetyl‑coenzyme A synthetase |
| RA | USA300TCH1516_ALE | 1,932,853 | T→C | I799V (ATT→GTT) | USA300HOU_RS09605 ← | hypothetical protein |
| RA | USA300TCH1516_ALE | 1,963,768 | C→G | V365L (GTA→CTA) | hemY ← | Protoporphyrinogen oxidase |
| RA | USA300TCH1516_ALE | 2,004,062 | (A)8→7 | intergenic (‑2285/+99) | USA300TCH1516_01884 ← / ← perR | tRNA‑Ile/Peroxide‑responsive repressor PerR |
| RA | USA300TCH1516_ALE | 2,010,363 | C→T | C146Y (TGT→TAT) | USA300HOU_RS10125 ← | Putative multidrug export ATP‑binding/permease protein |
| RA | USA300TCH1516_ALE | 2,018,612 | G→A | R103* (CGA→TGA) | mgt ← | Monofunctional glycosyltransferase |
| RA | USA300TCH1516_ALE | 2,078,573 | (T)7→8 | coding (246/681 nt) | USA300HOU_RS10490 ← | hypothetical protein |
| RA | USA300TCH1516_ALE | 2,079,114 | T→C | H201R (CAC→CGC) | natA_1 ← | ABC transporter ATP‑binding protein NatA |
| RA | USA300TCH1516_ALE | 2,086,905 | (A)8→7 | intergenic (‑56/‑629) | scn_3 ← / → chp | Staphylococcal complement inhibitor/Chemotaxis inhibitory protein |
| RA | USA300TCH1516_ALE | 2,272,733 | C→T | intergenic (‑339/‑342) | glmS ← / → mtlA | Glutamine‑‑fructose‑6‑phosphate aminotransferase [isomerizing]/PTS system mannitol‑specific EIICB component |
| RA | USA300TCH1516_ALE | 2,279,705 | G→A | A943V (GCA→GTA) | ebh_3 ← | Extracellular matrix‑binding protein ebh |
| RA | USA300TCH1516_ALE | 2,352,815 | G→A | A92V (GCA→GTA) | rpsI ← | 30S ribosomal protein S9 |
| RA | USA300TCH1516_ALE | 2,454,626 | A→T | L48L (CTA→CTT) | lyrA → | Lysostaphin resistance protein A |
| RA | USA300TCH1516_ALE | 2,502,887 | (A)5→6 | coding (1411/2106 nt) | melR_2 → | Melibiose operon regulatory protein |
| RA | USA300TCH1516_ALE | 2,532,298 | A→T | T15T (ACA→ACT) | femA_3 → | Aminoacyltransferase FemA |
| RA | USA300TCH1516_ALE | 2,543,088 | G→A | R283K (AGA→AAA) | hlgA → | Gamma‑hemolysin component A |
| RA | USA300TCH1516_ALE | 2,679,462 | (A)8→7 | intergenic (+334/‑55) | USA300HOU_RS13790 → / → ssaA2_4 | hypothetical protein/Staphylococcal secretory antigen ssaA2 |
| RA | USA300TCH1516_ALE | 2,709,444 | (T)6→5 | coding (1483/1812 nt) | oatA_2 ← | O‑acetyltransferase OatA |
| RA | USA300TCH1516_ALE | 2,750,562 | T→C | V197V (GTA→GTG) | betA ← | Oxygen‑dependent choline dehydrogenase |
| RA | USA300TCH1516_ALE | 2,787,510 | T→C | intergenic (+56/‑184) | zipA_3 → / → manR_2 | Cell division protein ZipA/Transcriptional regulator ManR |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | USA300TCH1516_ALE | 512620 = | 44 (1.000) | 34 (1.070) +40 bp |
22/212 | 0.2 | 51.6% | 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 | |||||