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 |
| MC | NC_012417 | 1 | Δ3,125 bp | 100% | USA300HOU_RS14890–USA300HOU_RS14900 | USA300HOU_RS14890, USA300HOU_RS15665, USA300HOU_RS14895, USA300HOU_RS14900 | |
| RA | USA300TCH1516_ALE | 39,378 | C→A | 100% | D586Y (GAT→TAT) | pbp ← | Beta‑lactam‑inducible penicillin‑binding protein |
| RA | USA300TCH1516_ALE | 110,660 | T→A | 19.4% | I173I (ATT→ATA) | USA300HOU_RS00515 → | putative lipoprotein |
| RA | USA300TCH1516_ALE | 111,512 | A→G | 36.1% | S194S (TCA→TCG) | USA300HOU_RS00520 → | putative lipoprotein |
| RA | USA300TCH1516_ALE | 111,516 | C→A | 34.1% | Q196K (CAA→AAA) | USA300HOU_RS00520 → | putative lipoprotein |
| RA | USA300TCH1516_ALE | 198,135 | T→A | 36.7% | S63R (AGT→AGA) | ssuC → | Putative aliphatic sulfonates transport permease protein SsuC |
| RA | USA300TCH1516_ALE | 367,644 | G→T | 100% | intergenic (‑96/‑62) | nanA ← / → bglK | N‑acetylneuraminate lyase/Beta‑glucoside kinase |
| RA | USA300TCH1516_ALE | 463,014 | C→A | 100% | E47* (GAA→TAA) | USA300HOU_RS02190 ← | hypothetical protein |
| RA | USA300TCH1516_ALE | 469,786 | A→G | 100% | G118G (GGA→GGG) | lpl2_6 → | putative lipoprotein |
| RA | USA300TCH1516_ALE | 479,553 | G→A | 100% | A194T (GCA→ACA) | USA300HOU_RS02280 → | hypothetical protein |
| RA | USA300TCH1516_ALE | 512,643 | A→G | 57.5% | intergenic (+711/‑6052) | recR → / → speA_2 | Recombination protein RecR/Arginine decarboxylase |
| RA | USA300TCH1516_ALE | 638,614 | G→T | 100% | T14K (ACA→AAA) | pdxK ← | Pyridoxine kinase |
| RA | USA300TCH1516_ALE | 642,696 | T→A | 36.5% | Q219H (CAA→CAT) | yjjP_1 ← | Inner membrane protein YjjP |
| RA | USA300TCH1516_ALE | 707,879 | A→T | 100% | L11I (TTA→ATA) | znuC_1 ← | High‑affinity zinc uptake system ATP‑binding protein ZnuC |
| RA | USA300TCH1516_ALE | 790,778 | G→A | 100% | intergenic (+277/‑197) | kipA_1 → / → ltaS | KipI antagonist/Lipoteichoic acid synthase |
| RA | USA300TCH1516_ALE | 979,234 | G→T | 16.2% | M838I (ATG→ATT) | clpB_1 → | Chaperone protein ClpB |
| RA | USA300TCH1516_ALE | 990,149 | C→G | 33.0% | S14C (TCC→TGC) | oppD_2 → | Oligopeptide transport ATP‑binding protein OppD |
| RA | USA300TCH1516_ALE | 1,232,465 | G→C | 100% | A124P (GCG→CCG) | prkC → | Serine/threonine‑protein kinase PrkC |
| RA | USA300TCH1516_ALE | 1,416,458 | A→T | 100% | I216N (ATT→AAT) | oppD_4 ← | Oligopeptide transport ATP‑binding protein OppD |
| RA | USA300TCH1516_ALE | 1,440,007 | Δ1 bp | 100% | coding (34/201 nt) | cspA_2 ← | Cold shock protein CspA |
| RA | USA300TCH1516_ALE | 1,474,639 | C→G | 100% | A9129P (GCA→CCA) | ebh_1 ← | Extracellular matrix‑binding protein ebh |
| RA | USA300TCH1516_ALE | 1,481,355 | G→T | 100% | A6890E (GCA→GAA) | ebh_1 ← | Extracellular matrix‑binding protein ebh |
| 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 | 1,744,454 | C→T | 100% | G73D (GGC→GAC) | apt ← | Adenine phosphoribosyltransferase |
| RA | USA300TCH1516_ALE | 1,797,772 | G→C | 100% | R7G (CGC→GGC) | phoR ← | Alkaline phosphatase synthesis sensor protein PhoR |
| RA | USA300TCH1516_ALE | 1,909,155 | G→A | 29.5% | intergenic (‑221/‑39) | tal ← / → USA300HOU_RS09460 | Transaldolase/hypothetical protein |
| JC | USA300TCH1516_ALE | 1,909,272 | Δ48 bp | 28.0% | coding (79‑126/303 nt) | USA300HOU_RS09460 → | hypothetical protein |
| RA | USA300TCH1516_ALE | 2,010,363 | C→T | 100% | C146Y (TGT→TAT) | USA300HOU_RS10125 ← | Putative multidrug export ATP‑binding/permease protein |
| JC | USA300TCH1516_ALE | 2,014,512 | +TAAAG | 26.4% | coding (686/837 nt) | USA300HOU_RS10150 ← | hypothetical protein |
| RA | USA300TCH1516_ALE | 2,021,817 | C→T | 100% | V139I (GTT→ATT) | USA300HOU_RS10190 ← | putative acyl‑CoA thioester hydrolase |
| RA | USA300TCH1516_ALE | 2,027,751 | C→G | 100% | V66L (GTA→CTA) | vraS ← | Sensor protein VraS |
| RA | USA300TCH1516_ALE | 2,225,018 | C→G | 7.7% | V53L (GTA→CTA) | atpA ← | ATP synthase subunit alpha |
| RA | USA300TCH1516_ALE | 2,279,705 | G→A | 100% | A943V (GCA→GTA) | ebh_3 ← | Extracellular matrix‑binding protein ebh |
| RA | USA300TCH1516_ALE | 2,289,252 | C→A | 100% | A80S (GCT→TCT) | cdaA ← | Cyclic di‑AMP synthase CdaA |
| RA | USA300TCH1516_ALE | 2,360,799 | A→G | 100% | G66G (GGT→GGC) | adk ← | Adenylate kinase |
| RA | USA300TCH1516_ALE | 2,372,863 | C→G | 35.1% | G305R (GGA→CGA) | pbuG ← | Guanine/hypoxanthine permease PbuG |
| RA | USA300TCH1516_ALE | 2,503,491 | C→G | 31.2% | T672R (ACG→AGG) | melR_2 → | Melibiose operon regulatory protein |
| RA | USA300TCH1516_ALE | 2,532,298 | A→T | 100% | T15T (ACA→ACT) | femA_3 → | Aminoacyltransferase FemA |
| RA | USA300TCH1516_ALE | 2,679,710 | G→T | 100% | G65V (GGC→GTC) | ssaA2_4 → | Staphylococcal secretory antigen ssaA2 |
| RA | USA300TCH1516_ALE | 2,709,297 | T→A | 28.0% | K544* (AAA→TAA) | oatA_2 ← | O‑acetyltransferase OatA |
| RA | USA300TCH1516_ALE | 2,709,919 | G→T | 31.3% | Y336* (TAC→TAA) | oatA_2 ← | O‑acetyltransferase OatA |
| RA | USA300TCH1516_ALE | 2,856,087 | T→A | 100% | P80P (CCT→CCA) | rpoA_2 → | DNA‑directed RNA polymerase subunit alpha |
| RA | USA300TCH1516_ALE | 2,864,675 | G→T | 13.7% | G16V (GGT→GTT) | cspLA → | Cold shock‑like protein CspLA |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | CP000731 | 1 | 12780–12561 | 12561–12780 | NA [0] | [1] 2 | repA–[USA300HOU_pUSA300HOUMR0016] | repA,USA300HOU_pUSA300HOUMR0003,USA300HOU_pUSA300HOUMR0004,USA300HOU_pUSA300HOUMR0005,USA300HOU_pUSA300HOUMR0006,cadR,cadX,USA300HOU_pUSA300HOUMR0010,blaZ,blaR,blaI,USA300HOU_pUSA300HOUMR0014,USA300HOU_pUSA300HOUMR0015,[USA300HOU_pUSA300HOUMR0016] |
| * | * | ÷ | CP000731 | 12890–12924 | 20483 | 7560–7594 | 2 [1] | [1] 2 | [USA300HOU_pUSA300HOUMR0016]–[USA300HOU_pUSA300HOUMR0027] | [USA300HOU_pUSA300HOUMR0016],USA300HOU_pUSA300HOUMR0018,USA300HOU_pUSA300HOUMR0019,USA300HOU_pUSA300HOUMR0021,USA300HOU_pUSA300HOUMR0023,USA300HOU_pUSA300HOUMR0024,[USA300HOU_pUSA300HOUMR0027] |
| * | * | ÷ | CP000731 | 20590 | 27041 | 6452 | 2 [1] | [0] NA | [USA300HOU_pUSA300HOUMR0027]–USA300HOU_pUSA300HOUMR0033 | [USA300HOU_pUSA300HOUMR0027],USA300HOU_pUSA300HOUMR0028,USA300HOU_pUSA300HOUMR0029,USA300HOU_pUSA300HOUMR0030,USA300HOU_pUSA300HOUMR0031,USA300HOU_pUSA300HOUMR0032,USA300HOU_pUSA300HOUMR0033 |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | USA300TCH1516_ALE | 512620 = | 31 (1.020) | 27 (1.290) +40 bp |
22/178 | NT | 55.9% | 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 | 2085296 = | 15 (0.490) | 4 (0.150) | 4/230 | NT | 19.3% | coding (173/201 nt) | hlb_1 | Phospholipase C |
| ? | USA300TCH1516_ALE | = 2128343 | 20 (0.740) | coding (1/825 nt) | hlb_2 | Phospholipase C | |||||
| * | ? | USA300TCH1516_ALE | = 2085309 | 13 (0.430) | 6 (0.220) | 6/230 | NT | 27.5% | coding (186/201 nt) | hlb_1 | Phospholipase C |
| ? | USA300TCH1516_ALE | 2128358 = | 20 (0.740) | coding (16/825 nt) | hlb_2 | Phospholipase C | |||||
| * | ? | USA300TCH1516_ALE | 2388283 = | 34 (1.120) | 3 (0.110) | 3/224 | NT | 10.3% | intergenic (+18/+84) | ribZ_1/sarV | Riboflavin transporter RibZ/HTH‑type transcriptional regulator SarV |
| ? | USA300TCH1516_ALE | 2388362 = | 23 (0.870) | intergenic (+97/+5) | ribZ_1/sarV | Riboflavin transporter RibZ/HTH‑type transcriptional regulator SarV | |||||