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 | annotation | gene | description |
RA | USA300TCH1516_ALE | 9,085 | G→A | R685H (CGT→CAT) | gyrA → | DNA gyrase subunit A |
RA | USA300TCH1516_ALE | 39,378 | C→A | D586Y (GAT→TAT) | 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 | 1,274,208 | C→T | S204L (TCA→TTA) | codY → | GTP‑sensing transcriptional pleiotropic repressor CodY |
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 |
RA | USA300TCH1516_ALE | 1,761,889 | C→A | D388Y (GAT→TAT) | fpgS ← | Folylpolyglutamate synthase |
RA | USA300TCH1516_ALE | 1,909,490 | +T | coding (297/303 nt) | USA300HOU_RS09460 → | hypothetical protein |
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 | 2,028,269 | G→C | P126A (CCA→GCA) | 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 | 2,352,815 | G→A | A92V (GCA→GTA) | rpsI ← | 30S ribosomal protein S9 |
RA | USA300TCH1516_ALE | 2,405,489 | G→T | intergenic (‑136/‑124) | USA300HOU_RS12375 ← / → ureA | Urea transporter/Urease subunit gamma |
RA | USA300TCH1516_ALE | 2,454,626 | A→T | L48L (CTA→CTT) | lyrA → | Lysostaphin resistance protein A |
RA | USA300TCH1516_ALE | 2,532,298 | A→T | T15T (ACA→ACT) | femA_3 → | Aminoacyltransferase FemA |
RA | USA300TCH1516_ALE | 2,679,725 | G→A | W70* (TGG→TAG) | ssaA2_4 → | Staphylococcal secretory antigen ssaA2 |
JC | USA300TCH1516_ALE | 2,709,677 | Δ12 bp | coding (1239‑1250/1812 nt) | oatA_2 ← | O‑acetyltransferase OatA |
Unassigned missing coverage evidence | ||||||||||
---|---|---|---|---|---|---|---|---|---|---|
seq id | start | end | size | ←reads | reads→ | gene | description | |||
* | * | ÷ | CP000731 | 1 | 303 | 303 | NA [0] | [1] 2 | [repA] | [repA] |
* | * | ÷ | CP000731 | 423 | 601 | 179 | 2 [1] | [1] 2 | repA | replication protein A |
* | * | ÷ | CP000731 | 1015 | 1141 | 127 | 2 [1] | [1] 2 | repA | replication protein A |
* | * | ÷ | CP000731 | 1646 | 1880 | 235 | 2 [1] | [1] 2 | repA/USA300HOU_pUSA300HOUMR0003 | replication protein A/hypothetical protein |
* | * | ÷ | CP000731 | 2251 | 2547 | 297 | 2 [1] | [1] 2 | [USA300HOU_pUSA300HOUMR0004] | [USA300HOU_pUSA300HOUMR0004] |
* | * | ÷ | CP000731 | 2810 | 2899 | 90 | 2 [1] | [1] 2 | USA300HOU_pUSA300HOUMR0004 | hypothetical protein |
* | * | ÷ | CP000731 | 3301 | 3391 | 91 | 2 [1] | [1] 2 | [USA300HOU_pUSA300HOUMR0005] | [USA300HOU_pUSA300HOUMR0005] |
* | * | ÷ | CP000731 | 3719 | 3931 | 213 | 2 [1] | [1] 2 | [USA300HOU_pUSA300HOUMR0006] | [USA300HOU_pUSA300HOUMR0006] |
* | * | ÷ | CP000731 | 4540 | 4813 | 274 | 2 [1] | [1] 2 | cadR | cadmium binding protein |
* | * | ÷ | CP000731 | 5038 | 5324 | 287 | 2 [1] | [1] 2 | [cadR]–[cadX] | [cadR],[cadX] |
* | * | ÷ | CP000731 | 5466 | 5510 | 45 | 2 [1] | [1] 2 | [cadX] | [cadX] |
* | * | ÷ | CP000731 | 6431 | 6582 | 152 | 2 [1] | [1] 2 | cadX/USA300HOU_pUSA300HOUMR0010 | cadmium efflux regulator/MarR family transcriptional regulator |
* | * | ÷ | CP000731 | 7077 | 7333 | 257 | 2 [1] | [1] 3 | USA300HOU_pUSA300HOUMR0010 | MarR family transcriptional regulator |
* | * | ÷ | CP000731 | 8444 | 8708 | 265 | 2 [1] | [1] 2 | blaZ | beta‑lactamase |
* | * | ÷ | CP000731 | 9484 | 9621 | 138 | 2 [1] | [1] 2 | blaR | beta‑lactamase regulator BlaR |
* | * | ÷ | CP000731 | 10306 | 10473 | 168 | 2 [1] | [1] 2 | blaR | beta‑lactamase regulator BlaR |
* | * | ÷ | CP000731 | 11175 | 11366 | 192 | 2 [1] | [0] 2 | [USA300HOU_pUSA300HOUMR0014] | [USA300HOU_pUSA300HOUMR0014] |
* | * | ÷ | CP000731 | 11508 | 11922 | 415 | 3 [1] | [1] 2 | [USA300HOU_pUSA300HOUMR0014] | [USA300HOU_pUSA300HOUMR0014] |
* | * | ÷ | CP000731 | 12064 | 12204 | 141 | 2 [1] | [1] 2 | USA300HOU_pUSA300HOUMR0015 | hypothetical protein |
* | * | ÷ | CP000731 | 12346 | 12460 | 115 | 2 [1] | [1] 2 | USA300HOU_pUSA300HOUMR0015/USA300HOU_pUSA300HOUMR0016 | hypothetical protein/IS257 transposase |
* | * | ÷ | CP000731 | 13376 | 13628 | 253 | 2 [1] | [1] 2 | USA300HOU_pUSA300HOUMR0016/USA300HOU_pUSA300HOUMR0018 | IS257 transposase/3',5' aminoglycoside phosphotransferase |
* | * | ÷ | CP000731 | 13710 | 13866 | 157 | 2 [1] | [1] 2 | USA300HOU_pUSA300HOUMR0016/USA300HOU_pUSA300HOUMR0018 | IS257 transposase/3',5' aminoglycoside phosphotransferase |
* | * | ÷ | CP000731 | 14773 | 14942 | 170 | 2 [1] | [1] 2 | USA300HOU_pUSA300HOUMR0018 | 3',5' aminoglycoside phosphotransferase |
* | * | ÷ | CP000731 | 15359 | 15591 | 233 | 2 [1] | [1] 2 | USA300HOU_pUSA300HOUMR0019 | strepthothricin acetyltransferase |
* | * | ÷ | CP000731 | 16098 | 16114 | 17 | 2 [1] | [1] 2 | USA300HOU_pUSA300HOUMR0019/USA300HOU_pUSA300HOUMR0021 | strepthothricin acetyltransferase/IS431 mec transposase |
* | * | ÷ | CP000731 | 16256 | 17675 | 1420 | 2 [1] | [1] 2 | USA300HOU_pUSA300HOUMR0021–[USA300HOU_pUSA300HOUMR0023] | USA300HOU_pUSA300HOUMR0021,[USA300HOU_pUSA300HOUMR0023] |
* | * | ÷ | CP000731 | 18400 | 18857 | 458 | 2 [0] | [1] 2 | USA300HOU_pUSA300HOUMR0024 | bacitracin ABC ATP binding cassette transporter, ABC protein |
* | * | ÷ | CP000731 | 18989 | 19244 | 256 | 2 [1] | [1] 2 | USA300HOU_pUSA300HOUMR0024/USA300HOU_pUSA300HOUMR0027 | bacitracin ABC ATP binding cassette transporter, ABC protein/IS431mec transposase |
* | * | ÷ | CP000731 | 19557 | 19824 | 268 | 2 [1] | [1] 2 | USA300HOU_pUSA300HOUMR0024/USA300HOU_pUSA300HOUMR0027 | bacitracin ABC ATP binding cassette transporter, ABC protein/IS431mec transposase |
* | * | ÷ | CP000731 | 20297 | 20513 | 217 | 3 [1] | [1] 2 | [USA300HOU_pUSA300HOUMR0027] | [USA300HOU_pUSA300HOUMR0027] |
* | * | ÷ | CP000731 | 20765–21078 | 21138 | 61–374 | 2 [1] | [1] 2 | [USA300HOU_pUSA300HOUMR0027] | [USA300HOU_pUSA300HOUMR0027] |
* | * | ÷ | CP000731 | 22234 | 22483 | 250 | 2 [1] | [1] 2 | USA300HOU_pUSA300HOUMR0028 | macrolide transporter |
* | * | ÷ | CP000731 | 22524 | 22799 | 276 | 2 [1] | [1] 2 | USA300HOU_pUSA300HOUMR0028 | macrolide transporter |
* | * | ÷ | CP000731 | 22941 | 23146 | 206 | 2 [1] | [1] 2 | [USA300HOU_pUSA300HOUMR0028]–[USA300HOU_pUSA300HOUMR0029] | [USA300HOU_pUSA300HOUMR0028],[USA300HOU_pUSA300HOUMR0029] |
* | * | ÷ | CP000731 | 23513 | 24013 | 501 | 2 [1] | [1] 2 | [USA300HOU_pUSA300HOUMR0029] | [USA300HOU_pUSA300HOUMR0029] |
* | * | ÷ | CP000731 | 24155 | 24310 | 156 | 2 [1] | [0] 2 | USA300HOU_pUSA300HOUMR0029/USA300HOU_pUSA300HOUMR0030 | macrolide 2'‑phosphotransferase/Sin recombinase |
* | * | ÷ | CP000731 | 24579 | 24718 | 140 | 2 [1] | [1] 2 | USA300HOU_pUSA300HOUMR0030 | Sin recombinase |
* | * | ÷ | CP000731 | 24860 | 24988 | 129 | 2 [1] | [1] 3 | USA300HOU_pUSA300HOUMR0030 | Sin recombinase |
* | * | ÷ | CP000731 | 26068 | 26301 | 234 | 2 [1] | [1] 2 | [USA300HOU_pUSA300HOUMR0033] | [USA300HOU_pUSA300HOUMR0033] |
* | * | ÷ | CP000731 | 26562 | 26762 | 201 | 2 [1] | [1] 2 | USA300HOU_pUSA300HOUMR0033 | partitioning protein |
* | * | ÷ | CP000731 | 26893 | 27041 | 149 | 2 [1] | [0] NA | USA300HOU_pUSA300HOUMR0033/– | partitioning protein/– |
Unassigned new junction evidence | |||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|
seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
* | ? | USA300TCH1516_ALE | 512620 = | 71 (1.130) | 58 (1.290) +40 bp |
42/200 | 0.1 | 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 |