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 | 25,663 | Δ1 bp | 100% | coding (316/333 nt) | USA300HOU_pUSA300HOUMR0031 → | hypothetical protein |
| RA | USA300TCH1516_ALE | 111,512 | A→G | 29.0% | S194S (TCA→TCG) | USA300HOU_RS00520 → | putative lipoprotein |
| RA | USA300TCH1516_ALE | 111,516 | C→A | 28.6% | Q196K (CAA→AAA) | USA300HOU_RS00520 → | putative lipoprotein |
| RA | USA300TCH1516_ALE | 148,138 | A→G | 8.4% | intergenic (+296/‑49) | butA → / → wbgU | Diacetyl reductase [(S)‑acetoin forming]/UDP‑N‑acetylglucosamine 4‑epimerase |
| RA | USA300TCH1516_ALE | 293,940 | C→T | 20.1% | intergenic (+57/‑471) | gatD → / → tarI' | Galactitol‑1‑phosphate 5‑dehydrogenase/Ribitol‑5‑phosphate cytidylyltransferase 2 |
| RA | USA300TCH1516_ALE | 478,502 | C→A | 100% | D342E (GAC→GAA) | nuoL → | NADH‑quinone oxidoreductase subunit L |
| RA | USA300TCH1516_ALE | 512,643 | A→G | 57.5% | intergenic (+711/‑6052) | recR → / → speA_2 | Recombination protein RecR/Arginine decarboxylase |
| RA | USA300TCH1516_ALE | 526,744 | C→T | 8.9% | R355C (CGT→TGT) | metG → | Methionine‑‑tRNA ligase |
| RA | USA300TCH1516_ALE | 529,100 | A→G | 8.0% | K159E (AAA→GAA) | rnmV_1 → | Ribonuclease M5 |
| RA | USA300TCH1516_ALE | 584,121 | G→T | 100% | intergenic (+205/‑67) | rplA → / → rplJ | 50S ribosomal protein L1/50S ribosomal protein L10 |
| RA | USA300TCH1516_ALE | 707,909 | A→T | 100% | M1M (TTG→ATG) † | znuC_1 ← | High‑affinity zinc uptake system ATP‑binding protein ZnuC |
| RA | USA300TCH1516_ALE | 736,763 | A→G | 9.1% | I415M (ATA→ATG) | bceB_1 → | Bacitracin export permease protein BceB |
| 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 | 990,792 | A→G | 12.5% | A228A (GCA→GCG) | oppD_2 → | Oligopeptide transport ATP‑binding protein OppD |
| RA | USA300TCH1516_ALE | 1,002,200 | T→G | 100% | M173R (ATG→AGG) | mecA → | Adapter protein MecA 1 |
| RA | USA300TCH1516_ALE | 1,076,774 | T→C | 19.2% | W51R (TGG→CGG) | purL → | Phosphoribosylformylglycinamidine synthase subunit PurL |
| RA | USA300TCH1516_ALE | 1,105,994 | T→C | 100% | T12T (ACT→ACC) | pdhD → | Dihydrolipoyl dehydrogenase |
| RA | USA300TCH1516_ALE | 1,194,918 | A→G | 11.7% | S290G (AGT→GGT) | ftsA → | Cell division protein FtsA |
| RA | USA300TCH1516_ALE | 1,196,508 | C→A | 100% | S338Y (TCT→TAT) | ftsZ → | Cell division protein FtsZ |
| 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 | 1,680,793 | A→G | 11.5% | I15I (ATT→ATC) | dgkA ← | Undecaprenol kinase |
| RA | USA300TCH1516_ALE | 1,744,473 | C→T | 100% | A67T (GCT→ACT) | apt ← | Adenine phosphoribosyltransferase |
| RA | USA300TCH1516_ALE | 2,010,363 | C→T | 100% | C146Y (TGT→TAT) | USA300HOU_RS10125 ← | Putative multidrug export ATP‑binding/permease protein |
| RA | USA300TCH1516_ALE | 2,153,482 | T→C | 10.8% | K254K (AAA→AAG) | treR_3 ← | HTH‑type transcriptional regulator TreR |
| RA | USA300TCH1516_ALE | 2,279,705 | G→A | 100% | A943V (GCA→GTA) | ebh_3 ← | Extracellular matrix‑binding protein ebh |
| RA | USA300TCH1516_ALE | 2,289,113 | T→C | 14.4% | Q126R (CAA→CGA) | cdaA ← | Cyclic di‑AMP synthase CdaA |
| RA | USA300TCH1516_ALE | 2,337,959 | C→T | 100% | intergenic (‑125/‑283) | adhR ← / → USA300HOU_RS11940 | HTH‑type transcriptional regulator AdhR/Hyaluronate lyase |
| RA | USA300TCH1516_ALE | 2,343,438 | C→T | 40.1% | intergenic (+114/+250) | USA300HOU_RS11955 → / ← aldC_1 | 65 kDa membrane protein/Alpha‑acetolactate decarboxylase |
| RA | USA300TCH1516_ALE | 2,455,692 | Δ1 bp | 100% | coding (1210/1260 nt) | lyrA → | Lysostaphin resistance protein A |
| RA | USA300TCH1516_ALE | 2,455,698 | 2 bp→AT | 100% | coding (1216‑1217/1260 nt) | lyrA → | Lysostaphin resistance protein A |
| RA | USA300TCH1516_ALE | 2,463,475 | T→C | 14.8% | intergenic (+316/‑21) | USA300HOU_RS12680 → / → gltS | Putative 3‑methyladenine DNA glycosylase/Sodium/glutamate symporter |
| RA | USA300TCH1516_ALE | 2,532,298 | A→T | 100% | T15T (ACA→ACT) | femA_3 → | Aminoacyltransferase FemA |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | USA300TCH1516_ALE | 2176701–2181115 | 2181115 | 1–4415 | 7 [6] | [6] 7 | ilvA/USA300TCH1516_02069 | L‑threonine dehydratase biosynthetic IlvA/tRNA‑Gly |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | USA300TCH1516_ALE | 512620 = | 25 (0.850) | 25 (1.240) +40 bp |
19/180 | NT | 59.2% | 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 | = 800928 | 27 (0.920) | 3 (0.110) | 3/246 | NT | 8.0% | intergenic (+62/‑289) | hisC_1/USA300HOU_RS03915 | Histidinol‑phosphate aminotransferase/Putative 5'(3')‑deoxyribonucleotidase |
| ? | USA300TCH1516_ALE | 801948 = | 43 (1.550) | intergenic (+189/+435) | USA300HOU_RS03915/USA300HOU_RS03920 | Putative 5'(3')‑deoxyribonucleotidase/Putative lipid kinase | |||||
| * | ? | USA300TCH1516_ALE | 2085296 = | 19 (0.650) | 4 (0.150) | 4/232 | NT | 17.4% | coding (173/201 nt) | hlb_1 | Phospholipase C |
| ? | USA300TCH1516_ALE | = 2128343 | 21 (0.800) | coding (1/825 nt) | hlb_2 | Phospholipase C | |||||