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 | 4,449 | C→A | 6.2% | Q171K (CAA→AAA) | recF → | DNA replication and repair protein RecF |
| RA | USA300TCH1516_ALE | 76,969 | G→A | 66.0% | intergenic (+509/‑107) | USA300HOU_RS00140 → / → USA300HOU_RS00350 | hypothetical protein/Monoacylglycerol lipase |
| RA | USA300TCH1516_ALE | 110,660 | T→A | 6.8% | I173I (ATT→ATA) | USA300HOU_RS00515 → | putative lipoprotein |
| RA | USA300TCH1516_ALE | 111,512 | A→G | 27.4% | S194S (TCA→TCG) | USA300HOU_RS00520 → | putative lipoprotein |
| RA | USA300TCH1516_ALE | 111,516 | C→A | 26.3% | Q196K (CAA→AAA) | USA300HOU_RS00520 → | putative lipoprotein |
| RA | USA300TCH1516_ALE | 111,560 | T→C | 10.7% | R210R (CGT→CGC) | USA300HOU_RS00520 → | putative lipoprotein |
| RA | USA300TCH1516_ALE | 162,116 | G→A | 8.5% | A205V (GCA→GTA) | phnE_2 ← | Phosphate‑import permease protein PhnE |
| RA | USA300TCH1516_ALE | 195,286 | T→A | 86.5% | intergenic (‑97/‑82) | USA300HOU_RS00900 ← / → USA300HOU_RS00905 | hypothetical protein/hypothetical protein |
| RA | USA300TCH1516_ALE | 215,097 | T→C | 5.2% | K164E (AAA→GAA) | argC ← | N‑acetyl‑gamma‑glutamyl‑phosphate reductase |
| RA | USA300TCH1516_ALE | 396,540 | G→A | 85.9% | A208T (GCA→ACA) | efeM → | putative iron uptake system component EfeM |
| RA | USA300TCH1516_ALE | 405,184 | C→A | 5.8% | W61L (TGG→TTG) | USA300HOU_RS01870 ← | hypothetical protein |
| RA | USA300TCH1516_ALE | 434,310 | A→T | 7.5% | L72* (TTA→TAA) | USA300HOU_RS02040 ← | hypothetical protein |
| RA | USA300TCH1516_ALE | 512,643 | A→G | 43.0% | intergenic (+711/‑6052) | recR → / → speA_2 | Recombination protein RecR/Arginine decarboxylase |
| RA | USA300TCH1516_ALE | 602,466 | G→T | 8.2% | intergenic (+56/‑104) | hchA → / → araB | Molecular chaperone Hsp31 and glyoxalase 3/Ribulokinase |
| RA | USA300TCH1516_ALE | 607,884 | G→A | 89.6% | R209* (CGA→TGA) | dck ← | Deoxyadenosine/deoxycytidine kinase |
| RA | USA300TCH1516_ALE | 629,681 | C→A | 71.2% | L84I (CTA→ATA) | USA300HOU_RS02990 → | 3‑hexulose‑6‑phosphate synthase |
| RA | USA300TCH1516_ALE | 665,392 | T→G | 84.0% | L79* (TTA→TGA) | paiA_1 → | Spermidine/spermine N(1)‑acetyltransferase |
| RA | USA300TCH1516_ALE | 707,910 | A→G | 83.0% | intergenic (‑1/‑121) | znuC_1 ← / → ideR | High‑affinity zinc uptake system ATP‑binding protein ZnuC/Iron‑dependent repressor IdeR |
| RA | USA300TCH1516_ALE | 863,781 | A→G | 5.0% | intergenic (+310/‑30) | eno → / → USA300HOU_RS04210 | Enolase/hypothetical protein |
| RA | USA300TCH1516_ALE | 951,713 | G→T | 9.8% | intergenic (+218/‑90) | USA300HOU_RS04740 → / → rocD2_2 | putative oxidoreductase/Ornithine aminotransferase 2 |
| RA | USA300TCH1516_ALE | 1,233,504 | T→A | 83.1% | V470D (GTT→GAT) | prkC → | Serine/threonine‑protein kinase PrkC |
| RA | USA300TCH1516_ALE | 1,265,591 | C→T | 7.9% | intergenic (+99/‑74) | femA_1 → / → dprA | Aminoacyltransferase FemA/DNA processing protein DprA |
| 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 | 89.0% | 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 | 1,646,189 | G→C | 100% | A155G (GCA→GGA) | ypdF ← | Aminopeptidase YpdF |
| RA | USA300TCH1516_ALE | 1,646,545 | G→A | 6.4% | T36T (ACC→ACT) | ypdF ← | Aminopeptidase YpdF |
| RA | USA300TCH1516_ALE | 1,744,362 | G→A | 92.4% | H104Y (CAC→TAC) | apt ← | Adenine phosphoribosyltransferase |
| RA | USA300TCH1516_ALE | 1,761,889 | C→A | 78.6% | D388Y (GAT→TAT) | fpgS ← | Folylpolyglutamate synthase |
| RA | USA300TCH1516_ALE | 1,963,768 | C→G | 90.1% | 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 | 2,279,705 | G→A | 100% | A943V (GCA→GTA) | ebh_3 ← | Extracellular matrix‑binding protein ebh |
| RA | USA300TCH1516_ALE | 2,352,815 | G→A | 84.5% | A92V (GCA→GTA) | rpsI ← | 30S ribosomal protein S9 |
| RA | USA300TCH1516_ALE | 2,454,626 | A→T | 74.9% | L48L (CTA→CTT) | lyrA → | Lysostaphin resistance protein A |
| RA | USA300TCH1516_ALE | 2,532,298 | A→T | 100% | T15T (ACA→ACT) | femA_3 → | Aminoacyltransferase FemA |
| RA | USA300TCH1516_ALE | 2,725,352 | A→T | 6.5% | intergenic (‑58/+276) | USA300HOU_RS14015 ← / ← USA300HOU_RS14020 | Baeyer‑Villiger flavin‑containing monooxygenase/hypothetical protein |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | USA300TCH1516_ALE | 512620 = | 102 (1.170) | 66 (1.090) +40 bp |
48/180 | NT | 48.4% | 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 | |||||