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 | 8,740 | T→C | 100% | I8V (ATT→GTT) | blaZ ← | beta‑lactamase |
| RA | CP000731 | 25,663 | Δ1 bp | 100% | coding (316/333 nt) | USA300HOU_pUSA300HOUMR0031 → | hypothetical protein |
| RA | USA300TCH1516_ALE | 4,873 | T→A | 6.8% | I312N (ATC→AAC) | recF → | DNA replication and repair protein RecF |
| RA | USA300TCH1516_ALE | 39,195 | T→C | 62.2% | K647E (AAA→GAA) | pbp ← | Beta‑lactam‑inducible penicillin‑binding protein |
| RA | USA300TCH1516_ALE | 39,378 | C→T | 100% | D586N (GAT→AAT) | pbp ← | Beta‑lactam‑inducible penicillin‑binding protein |
| RA | USA300TCH1516_ALE | 39,888 | T→C | 19.2% | N416D (AAC→GAC) | pbp ← | Beta‑lactam‑inducible penicillin‑binding protein |
| RA | USA300TCH1516_ALE | 42,835 | T→C | 28.2% | Q377Q (CAA→CAG) | USA300TCH1516_00035 ← | hypothetical protein |
| RA | USA300TCH1516_ALE | 76,969 | G→A | 100% | intergenic (+509/‑107) | USA300HOU_RS00140 → / → USA300HOU_RS00350 | hypothetical protein/Monoacylglycerol lipase |
| RA | USA300TCH1516_ALE | 93,268 | G→A | 76.9% | A73T (GCT→ACT) | glpE → | Thiosulfate sulfurtransferase GlpE |
| RA | USA300TCH1516_ALE | 111,512 | A→G | 35.5% | S194S (TCA→TCG) | USA300HOU_RS00520 → | putative lipoprotein |
| RA | USA300TCH1516_ALE | 111,516 | C→A | 37.4% | Q196K (CAA→AAA) | USA300HOU_RS00520 → | putative lipoprotein |
| RA | USA300TCH1516_ALE | 111,560 | T→C | 19.6% | R210R (CGT→CGC) | USA300HOU_RS00520 → | putative lipoprotein |
| RA | USA300TCH1516_ALE | 129,796 | G→C | 100% | intergenic (‑209/+212) | spa ← / ← sarS | Immunoglobulin G‑binding protein A/HTH‑type transcriptional regulator SarS |
| RA | USA300TCH1516_ALE | 169,407 | G→A | 100% | G82E (GGA→GAA) | repE → | Replication initiation protein |
| RA | USA300TCH1516_ALE | 195,286 | T→A | 100% | intergenic (‑97/‑82) | USA300HOU_RS00900 ← / → USA300HOU_RS00905 | hypothetical protein/hypothetical protein |
| RA | USA300TCH1516_ALE | 256,718 | C→T | 13.0% | E219K (GAA→AAA) | USA300HOU_RS01135 ← | putative response regulatory protein |
| RA | USA300TCH1516_ALE | 283,980 | A→G | 9.5% | intergenic (+205/+115) | ldh1 → / ← ptsG_2 | L‑lactate dehydrogenase 1/PTS system glucose‑specific EIICBA component |
| RA | USA300TCH1516_ALE | 396,540 | G→A | 100% | A208T (GCA→ACA) | efeM → | putative iron uptake system component EfeM |
| RA | USA300TCH1516_ALE | 512,643 | A→G | 43.5% | intergenic (+711/‑6052) | recR → / → speA_2 | Recombination protein RecR/Arginine decarboxylase |
| RA | USA300TCH1516_ALE | 536,758 | C→T | 100% | P202L (CCA→CTA) | rplY → | 50S ribosomal protein L25 |
| RA | USA300TCH1516_ALE | 607,884 | G→A | 100% | R209* (CGA→TGA) | dck ← | Deoxyadenosine/deoxycytidine kinase |
| RA | USA300TCH1516_ALE | 618,567 | T→C | 18.0% | D1223D (GAT→GAC) | sdrD → | Serine‑aspartate repeat‑containing protein D |
| 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 | 673,010 | T→C | 12.1% | G78G (GGT→GGC) | btuF → | Vitamin B12‑binding protein |
| 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 | 744,375 | A→T | 100% | I506F (ATT→TTT) | melR_1 → | Melibiose operon regulatory protein |
| RA | USA300TCH1516_ALE | 749,249 | C→T | 100% | S59S (AGC→AGT) | setC → | Sugar efflux transporter C |
| RA | USA300TCH1516_ALE | 860,576 | C→T | 10.0% | S19S (AGC→AGT) | gpmI → | 2,3‑bisphosphoglycerate‑independent phosphoglycerate mutase |
| RA | USA300TCH1516_ALE | 1,017,678 | T→C | 59.6% | F391S (TTC→TCC) | acp → | Sodium/proton‑dependent alanine carrier protein |
| RA | USA300TCH1516_ALE | 1,063,909:1 | +C | 100% | coding (580/1218 nt) | ywtF ← | Putative transcriptional regulator YwtF |
| RA | USA300TCH1516_ALE | 1,125,066 | G→C | 100% | E729Q (GAG→CAG) | cfiB_1 → | 2‑oxoglutarate carboxylase small subunit |
| RA | USA300TCH1516_ALE | 1,233,504 | T→A | 100% | V470D (GTT→GAT) | prkC → | Serine/threonine‑protein kinase PrkC |
| RA | USA300TCH1516_ALE | 1,298,108 | T→A | 100% | intergenic (+4/‑232) | pnp → / → rnj2 | Polyribonucleotide nucleotidyltransferase/Ribonuclease J 2 |
| RA | USA300TCH1516_ALE | 1,324,248 | Δ1 bp | 100% | coding (1020/2010 nt) | mutL → | DNA mismatch repair protein MutL |
| 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 | 1,448,805 | T→C | 12.8% | N153D (AAT→GAT) | mhqA_2 ← | Putative ring‑cleaving dioxygenase MhqA |
| RA | USA300TCH1516_ALE | 1,489,621 | C→A | 16.5% | A4135S (GCT→TCT) | ebh_1 ← | Extracellular matrix‑binding protein ebh |
| RA | USA300TCH1516_ALE | 1,499,376 | C→A | 100% | G883V (GGT→GTT) | ebh_1 ← | Extracellular matrix‑binding protein ebh |
| RA | USA300TCH1516_ALE | 1,513,930 | A→T | 100% | L413F (TTA→TTT) | USA300HOU_RS07375 → | hypothetical protein |
| RA | USA300TCH1516_ALE | 1,514,843 | G→A | 13.8% | Y319Y (TAC→TAT) | rlmL ← | Ribosomal RNA large subunit methyltransferase L |
| RA | USA300TCH1516_ALE | 1,610,233 | A→G | 11.5% | S214P (TCT→CCT) | srrB ← | Sensor protein SrrB |
| RA | USA300TCH1516_ALE | 1,613,762 | T→C | 100% | intergenic (‑31/‑37) | scpA ← / → USA300HOU_RS08000 | Segregation and condensation protein A/hypothetical protein |
| RA | USA300TCH1516_ALE | 1,624,673 | T→A | 100% | K192I (AAA→ATA) | malL ← | Oligo‑1,6‑glucosidase |
| RA | USA300TCH1516_ALE | 1,646,189 | G→C | 100% | A155G (GCA→GGA) | ypdF ← | Aminopeptidase YpdF |
| RA | USA300TCH1516_ALE | 1,657,158 | C→T | 38.9% | G174S (GGT→AGT) | comGA ← | ComG operon protein 1 |
| RA | USA300TCH1516_ALE | 1,724,706 | G→T | 13.0% | P192T (CCA→ACA) | alaS ← | Alanine‑‑tRNA ligase |
| RA | USA300TCH1516_ALE | 1,744,362 | G→A | 100% | H104Y (CAC→TAC) | apt ← | Adenine phosphoribosyltransferase |
| RA | USA300TCH1516_ALE | 1,761,889 | C→A | 100% | D388Y (GAT→TAT) | fpgS ← | Folylpolyglutamate synthase |
| RA | USA300TCH1516_ALE | 1,830,883 | C→T | 75.3% | K79K (AAG→AAA) | ezrA ← | Septation ring formation regulator EzrA |
| RA | USA300TCH1516_ALE | 1,851,260 | C→A | 100% | A115S (GCG→TCG) | acsA_1 ← | Acetyl‑coenzyme A synthetase |
| RA | USA300TCH1516_ALE | 1,854,250 | T→C | 13.8% | S145S (TCA→TCG) | ccpA ← | Catabolite control protein A |
| RA | USA300TCH1516_ALE | 1,932,853 | T→C | 100% | I799V (ATT→GTT) | 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 | 2,018,612 | G→A | 100% | R103* (CGA→TGA) | mgt ← | Monofunctional glycosyltransferase |
| RA | USA300TCH1516_ALE | 2,041,281 | T→C | 11.5% | intergenic (‑364/+405) | dagK ← / ← gatB_2 | Diacylglycerol kinase/Aspartyl/glutamyl‑tRNA(Asn/Gln) amidotransferase subunit B |
| RA | USA300TCH1516_ALE | 2,078,566:1 | +T | 100% | coding (253/681 nt) | USA300HOU_RS10490 ← | hypothetical protein |
| RA | USA300TCH1516_ALE | 2,079,114 | T→C | 69.0% | H201R (CAC→CGC) | natA_1 ← | ABC transporter ATP‑binding protein NatA |
| RA | USA300TCH1516_ALE | 2,186,228 | T→C | 34.9% | T129T (ACA→ACG) | rsbW ← | Serine‑protein kinase RsbW |
| 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 | 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 | 2,482,693 | T→C | 23.0% | A329A (GCT→GCC) | hssS → | Heme sensor protein HssS |
| RA | USA300TCH1516_ALE | 2,502,882:1 | +A | 100% | coding (1406/2106 nt) | melR_2 → | Melibiose operon regulatory protein |
| RA | USA300TCH1516_ALE | 2,532,298 | A→T | 100% | T15T (ACA→ACT) | femA_3 → | Aminoacyltransferase FemA |
| RA | USA300TCH1516_ALE | 2,543,088 | G→A | 100% | R283K (AGA→AAA) | hlgA → | Gamma‑hemolysin component A |
| RA | USA300TCH1516_ALE | 2,679,455 | Δ1 bp | 100% | intergenic (+327/‑62) | USA300HOU_RS13790 → / → ssaA2_4 | hypothetical protein/Staphylococcal secretory antigen ssaA2 |
| RA | USA300TCH1516_ALE | 2,709,439 | Δ1 bp | 100% | coding (1488/1812 nt) | oatA_2 ← | O‑acetyltransferase OatA |
| RA | USA300TCH1516_ALE | 2,750,562 | T→C | 100% | V197V (GTA→GTG) | betA ← | Oxygen‑dependent choline dehydrogenase |
| RA | USA300TCH1516_ALE | 2,778,338 | C→A | 12.6% | *314Y (TAG→TAT) | arcC2 ← | Carbamate kinase 2 |
| RA | USA300TCH1516_ALE | 2,784,861 | C→T | 10.8% | T309T (ACG→ACA) | aur ← | Zinc metalloproteinase aureolysin |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | USA300TCH1516_ALE | 37094 = | 41 (1.300) | 3 (0.100) | 3/240 | NT | 6.8% | intergenic (+118/‑719) | USA300HOU_RS14915/ugpQ_1 | hypothetical protein/Glycerophosphodiester phosphodiesterase, cytoplasmic |
| ? | USA300TCH1516_ALE | 37188 = | 45 (1.550) | intergenic (+212/‑625) | USA300HOU_RS14915/ugpQ_1 | hypothetical protein/Glycerophosphodiester phosphodiesterase, cytoplasmic | |||||
| * | ? | USA300TCH1516_ALE | 512620 = | 30 (0.950) | 25 (1.150) +40 bp |
18/180 | NT | 54.7% | 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 | |||||