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 | 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 | 92.5% | I8V (ATT→GTT) | blaZ ← | beta‑lactamase |
| RA | CP000731 | 25,663 | Δ1 bp | 100% | coding (316/333 nt) | USA300HOU_pUSA300HOUMR0031 → | hypothetical protein |
| RA | USA300TCH1516_ALE | 39,378 | C→T | 100% | D586N (GAT→AAT) | 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 | 15.7% | I173I (ATT→ATA) | USA300HOU_RS00515 → | putative lipoprotein |
| RA | USA300TCH1516_ALE | 111,512 | A→G | 26.6% | S194S (TCA→TCG) | USA300HOU_RS00520 → | putative lipoprotein |
| RA | USA300TCH1516_ALE | 111,516 | C→A | 25.7% | Q196K (CAA→AAA) | USA300HOU_RS00520 → | putative lipoprotein |
| RA | USA300TCH1516_ALE | 129,796 | G→C | 92.5% | intergenic (‑209/+212) | spa ← / ← sarS | Immunoglobulin G‑binding protein A/HTH‑type transcriptional regulator SarS |
| 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 | 512,643 | A→G | 53.8% | intergenic (+711/‑6052) | recR → / → speA_2 | Recombination protein RecR/Arginine decarboxylase |
| RA | USA300TCH1516_ALE | 536,758 | C→T | 91.5% | 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 | 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 | 725,415 | T→C | 8.6% | V101A (GTT→GCT) | dhaK → | PTS‑dependent dihydroxyacetone kinase, dihydroxyacetone‑binding subunit DhaK |
| RA | USA300TCH1516_ALE | 756,598 | T→A | 5.8% | intergenic (‑86/‑127) | uppP ← / → cydD | Undecaprenyl‑diphosphatase/ATP‑binding/permease protein CydD |
| RA | USA300TCH1516_ALE | 783,859 | T→C | 6.9% | intergenic (‑8/+91) | USA300HOU_RS03830 ← / ← queE_1 | hypothetical protein/7‑carboxy‑7‑deazaguanine synthase |
| RA | USA300TCH1516_ALE | 1,063,804:1 | +T | 72.3% | coding (685/1218 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 | 1,151,090 | A→G | 10.1% | K66K (AAA→AAG) | zapA → | Cell division protein ZapA |
| 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 | 1,375,713 | T→A | 7.8% | I280I (ATT→ATA) | sbcC → | Nuclease SbcCD subunit C |
| 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 | 1,499,376 | C→A | 90.3% | G883V (GGT→GTT) | ebh_1 ← | Extracellular matrix‑binding protein ebh |
| RA | USA300TCH1516_ALE | 1,509,090 | G→A | 7.6% | A1100V (GCT→GTT) | USA300HOU_RS07370 ← | Bacterial dynamin‑like protein |
| RA | USA300TCH1516_ALE | 1,513,930 | A→T | 100% | L413F (TTA→TTT) | USA300HOU_RS07375 → | 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 | 1,744,362 | 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 | 1,851,260 | C→A | 100% | A115S (GCG→TCG) | acsA_1 ← | Acetyl‑coenzyme A synthetase |
| 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 | 2,027,432 | G→A | 9.7% | A172V (GCT→GTT) | vraS ← | Sensor protein VraS |
| RA | USA300TCH1516_ALE | 2,083,309 | G→A | 8.5% | A477V (GCG→GTG) | USA300HOU_RS10525 ← | 65 kDa membrane protein |
| RA | USA300TCH1516_ALE | 2,108,728 | A→G | 9.8% | Y419Y (TAT→TAC) | USA300HOU_RS10675 ← | hypothetical protein |
| RA | USA300TCH1516_ALE | 2,256,068 | T→C | 5.0% | A144A (GCT→GCC) | deoD1 → | Purine nucleoside phosphorylase DeoD‑type 1 |
| RA | USA300TCH1516_ALE | 2,260,448 | G→T | 6.7% | P260H (CCT→CAT) | gmuF ← | putative mannose‑6‑phosphate isomerase GmuF |
| 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 | 2,429,206 | T→C | 7.8% | L147L (TTA→TTG) | lytR_2 ← | Transcriptional regulator LytR |
| RA | USA300TCH1516_ALE | 2,454,626 | A→T | 100% | L48L (CTA→CTT) | lyrA → | Lysostaphin resistance protein A |
| RA | USA300TCH1516_ALE | 2,504,989 | T→C | 7.0% | intergenic (+293/+111) | USA300HOU_RS12890 → / ← gltT | hypothetical protein/Proton/sodium‑glutamate symport 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 | 90.2% | R283K (AGA→AAA) | hlgA → | Gamma‑hemolysin component A |
| RA | USA300TCH1516_ALE | 2,796,110 | A→G | 8.1% | S86S (TCA→TCG) | USA300HOU_RS14370 → | N‑acetylmuramoyl‑L‑alanine amidase domain‑containing protein |
| RA | USA300TCH1516_ALE | 2,847,204 | A→G | 7.4% | H10R (CAC→CGC) | yceI → | Protein YceI |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | USA300TCH1516_ALE | 512620 = | 47 (0.880) | 37 (1.010) +40 bp |
30/180 | NT | 53.3% | 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 | = 825232 | 50 (0.940) | 4 (0.080) | 4/250 | NT | 7.5% | coding (24/1056 nt) | tagO | putative undecaprenyl‑phosphate N‑acetylglucosaminyl 1‑phosphate transferase |
| ? | USA300TCH1516_ALE | = 825273 | 51 (1.000) | coding (65/1056 nt) | tagO | putative undecaprenyl‑phosphate N‑acetylglucosaminyl 1‑phosphate transferase | |||||