breseq version 0.33.1 revision 8505477f25b3
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
Predicted mutations | ||||||
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evidence | seq id | position | mutation | annotation | gene | description |
RA | USA300TCH1516_ALE | 39,672 | C→A | V488F (GTT→TTT) | pbp ← | Beta‑lactam‑inducible penicillin‑binding protein |
RA | USA300TCH1516_ALE | 76,969 | G→A | intergenic (+509/‑107) | USA300HOU_RS00140 → / → USA300HOU_RS00350 | hypothetical protein/Monoacylglycerol lipase |
RA | USA300TCH1516_ALE | 195,286 | T→A | intergenic (‑97/‑82) | USA300HOU_RS00900 ← / → USA300HOU_RS00905 | hypothetical protein/hypothetical protein |
RA | USA300TCH1516_ALE | 396,540 | G→A | A208T (GCA→ACA) | efeM → | putative iron uptake system component EfeM |
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 | 804,673 | A→T | L135I (TTA→ATA) | dtpT ← | Di‑/tripeptide transporter |
RA | USA300TCH1516_ALE | 933,033 | T→C | intergenic (‑74/‑27) | nfuA ← / → USA300HOU_RS04645 | Fe/S biogenesis protein NfuA/hypothetical protein |
RA | USA300TCH1516_ALE | 1,064,445 | Δ1 bp | coding (44/1218 nt) | ywtF ← | Putative transcriptional regulator YwtF |
RA | USA300TCH1516_ALE | 1,233,504 | T→A | V470D (GTT→GAT) | prkC → | Serine/threonine‑protein kinase PrkC |
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 | 1,513,930 | A→T | L413F (TTA→TTT) | USA300HOU_RS07375 → | hypothetical protein |
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 |
JC | USA300TCH1516_ALE | 1,747,382 | (TAC)3→2 | coding (2065‑2067/2280 nt) | USA300HOU_RS08710 ← | Heme uptake protein MmpL11 |
RA | USA300TCH1516_ALE | 1,761,889 | C→A | D388Y (GAT→TAT) | fpgS ← | Folylpolyglutamate synthase |
RA | USA300TCH1516_ALE | 1,963,768 | C→G | V365L (GTA→CTA) | hemY ← | Protoporphyrinogen oxidase |
RA | USA300TCH1516_ALE | 2,010,363 | C→T | C146Y (TGT→TAT) | USA300HOU_RS10125 ← | Putative multidrug export ATP‑binding/permease protein |
RA | USA300TCH1516_ALE | 2,028,583 | G→T | A21D (GCC→GAC) | USA300HOU_RS10230 ← | hypothetical protein |
RA | USA300TCH1516_ALE | 2,279,705 | G→A | A943V (GCA→GTA) | ebh_3 ← | Extracellular matrix‑binding protein ebh |
RA | USA300TCH1516_ALE | 2,289,257 | A→C | V78G (GTA→GGA) | cdaA ← | Cyclic di‑AMP synthase CdaA |
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 |
MC JC | USA300TCH1516_ALE | 2,501,188 | Δ3,014 bp | melR_2–ydaG | melR_2, ydaG | |
RA | USA300TCH1516_ALE | 2,532,298 | A→T | T15T (ACA→ACT) | femA_3 → | Aminoacyltransferase FemA |
Unassigned missing coverage evidence | ||||||||||
---|---|---|---|---|---|---|---|---|---|---|
seq id | start | end | size | ←reads | reads→ | gene | description | |||
* | * | ÷ | CP000731 | 1 | 1342 | 1342 | NA [0] | [1] 2 | repA | repA |
* | * | ÷ | CP000731 | 1433 | 1562 | 130 | 2 [1] | [1] 2 | repA/USA300HOU_pUSA300HOUMR0003 | replication protein A/hypothetical protein |
* | * | ÷ | CP000731 | 1611 | 2246 | 636 | 342 [0] | [1] 2 | USA300HOU_pUSA300HOUMR0003 | USA300HOU_pUSA300HOUMR0003 |
* | * | ÷ | CP000731 | 2360–2386 | 4278–4274 | 1889–1919 | 2 [1] | [1] 3 | USA300HOU_pUSA300HOUMR0004–USA300HOU_pUSA300HOUMR0006 | USA300HOU_pUSA300HOUMR0004,USA300HOU_pUSA300HOUMR0005,USA300HOU_pUSA300HOUMR0006 |
* | * | ÷ | CP000731 | 4434 | 27041 | 22608 | 41 [1] | [0] NA | cadR–USA300HOU_pUSA300HOUMR0033 | cadR,cadX,USA300HOU_pUSA300HOUMR0010,blaZ,blaR,blaI,USA300HOU_pUSA300HOUMR0014,USA300HOU_pUSA300HOUMR0015,USA300HOU_pUSA300HOUMR0016,USA300HOU_pUSA300HOUMR0018,USA300HOU_pUSA300HOUMR0019,USA300HOU_pUSA300HOUMR0021,USA300HOU_pUSA300HOUMR0023,USA300HOU_pUSA300HOUMR0024,USA300HOU_pUSA300HOUMR0027,USA300HOU_pUSA300HOUMR0028,USA300HOU_pUSA300HOUMR0029,USA300HOU_pUSA300HOUMR0030,USA300HOU_pUSA300HOUMR0031,USA300HOU_pUSA300HOUMR0032,USA300HOU_pUSA300HOUMR0033 |
Unassigned new junction evidence | |||||||||||
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seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
* | ? | USA300TCH1516_ALE | 512620 = | 71 (0.800) | 54 (0.860) +40 bp |
35/198 | 0.5 | 51.7% | 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 |