Sample Resequencing Stats

Note: The mutation counts shown below represent unfiltered mutation sets.
ALE, Flask, Isolate Predicted Mutations Mean Coverage Total Reads Percent Mapped Mapped Reads Average Read Length
A6 F1 I0 R1 2892 75.3 5698161 66.1% 3766484 59.5

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 1,259,349 A→C 23.1% I525M (ATT→ATG) ‡ torZ ← trimethylamine N‑oxide reductase system III, catalytic subunit

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,259,3490AC23.1% 233.8 / 103.1 160I525M (ATT→ATG) ‡torZtrimethylamine N‑oxide reductase system III, catalytic subunit
Reads supporting (aligned to +/- strand):  ref base A (67/56);  new base C (17/20);  total (84/76)
Fisher's exact test for biased strand distribution p-value = 4.53e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.01e-01

Only 100 of 172 total aligned reads displayed.

AAGATCGGCAAACACGTCAAAATCGTTACGCGCTTCAAATTGCGGAGCAACAGCCTGCTTCATCGGCACAATATGCTGGTTGCTGTAATCACCGGTCATCGTCAAGTCATTGCGCTCAAACGATGTGGTGATCGGTAATA  >  minE/1259280‑1259419
                                                                     |                                                                      
  gATCGGCAAACACGTCAAAATCGTTACGCGCTTCAAATTGCGGAGCAACAGCCTGCTTCATCGGCACAata                                                                     >  1:2673821/1‑71 (MQ=255)
    tCGGCAAACACGTCAAAATCGTTACGCGCTTCAAATTGCGGAGCAACAGCCTGCTTCATCGGCACAatat                                                                    >  1:4082233/1‑70 (MQ=255)
         aaaaACATCAAAATCATTACGCGCTTCATAGCGTGGCGGCACCACTTGCTTCATCGGCACCAGATGCTgat                                                              <  1:3972096/71‑3 (MQ=255)
         aaaCACGTCAAAATCGTTACGCGCTTCAAATTGCGGAGCAACAGCCTGCTTCATCGGCACAATATGCTGGt                                                              <  1:5160103/71‑1 (MQ=255)
           acacGTCAAAATCGTTACGCGCTTCAAATTGCGGAGCAACAGCCTGCTTCATCGGCACaa                                                                       <  1:2597644/60‑1 (MQ=255)
             acGTCAAAATCGTTACGCGCTTCAAATTGCGGAGCAACAGCCTGCTTCATCGGCACAATATGCTGGTTGCt                                                          <  1:3570864/71‑1 (MQ=255)
              catCAAAATCATTACGCGCTTCATAGCGTGGCGGCACCACTTGCTTCATCGGCACCAGATGCTGATTACTg                                                         >  1:316453/3‑71 (MQ=255)
               atCAAAATCATTACGCGCTTCATAGCGTGGCGGCACCACTTGCTTCATCGGCACCAGATGCTgat                                                              <  1:1929920/64‑3 (MQ=255)
                tCAAAATCATTACGCGCTTCATAGCGTGGCGGCACCACTTGCTTCATCGGCACCAGATGCTGATTACTGTa                                                       <  1:832803/71‑1 (MQ=255)
                tCAAAATCATTACGCGCTTCATAGCGTGGCGGCACCACTTGCTTCATCGGCACCAGATGCTGATTACTGTa                                                       <  1:1980557/71‑1 (MQ=255)
                 cAAAATCGTTACGCGCTTCAAATTGCGGAGCAACAGCCTGCTTCATCGGCACAATATGCTGGTTGCTGTaa                                                      >  1:446779/1‑71 (MQ=255)
                  aaaaTCGTTACGCGCTTCAAATTGCGGAGCAACAGCCTGCTTCATCGGCACAATATGCTGGTTGCTGTaa                                                      >  1:1025002/1‑70 (MQ=255)
                  aaaaTCGTTACGCGCTTCAAATTGCGGAGCAACAGCCTGCTTCATCGGCACAATATGCTGGTTGCTGTAAt                                                     >  1:283912/1‑71 (MQ=255)
                  aaaaTCGTTACGCGCTTCAAATTGCGGAGCAACAGCCTGCTTCATCGGCACAATATGCTGGTTGCTGTAAt                                                     >  1:2360281/1‑71 (MQ=255)
                  aaaaTCATTACGCGCTTCATAGCGTGGCGGCACCACTTGCTTCATCGGCACCAGATGCTGAtta                                                            >  1:3493256/1‑63 (MQ=255)
                      tCGTTACGCGCTTCAAATTGCGGAGCAACAGCCTGCTTCATCGGCACAATATGCTGGTTGCt                                                          <  1:5148167/62‑1 (MQ=255)
                        gTTACGCGCTTAAAATTGCGGAGCAACAGCCTGCTTCATCGGCACAATATGCTGGTTGCTGTAATCACCgg                                               >  1:3466036/1‑71 (MQ=255)
                           aCGCGCTTCAAATTGCGGAGCAACAGCCTGCTTCATCGGCACAATATGCTGGTTGCTGTAATCACCGGTCa                                            >  1:836881/1‑71 (MQ=255)
                             gcgcTTCAAATTGCGGAGCAACAGCCTGCTTCATCGGCACAATATGCTGGTTGCTGTAATCACCGGTCATc                                          <  1:5524540/71‑1 (MQ=255)
                              cgcTTCAAATTGCGGAGCAACAGCCTGCTTCATCGGCACAATATg                                                                   >  1:5430121/1‑45 (MQ=255)
                               gcTTCAAATTGCGGAGCAACAGCCTGCTTCATCGGCACAATATGCTGGTTGCTGTAATCAc                                                  >  1:5050578/1‑61 (MQ=255)
                               gcTTCAAATTGCGGAGCAACAGCCTGCTTCATCGGCACAATATGCTGGTTGCTGTAATCACCGGTCATCGt                                        >  1:54923/1‑71 (MQ=255)
                                cTTCAAATTGCGGAGCAACAGCCTGCTTCATCGGCACAATATGCTGGTTGc                                                           <  1:3094771/51‑1 (MQ=255)
                                cTTCAAATTGCGGAGCAACAGCCTGCTTCATCGGCACAATATGCTGGTTGCt                                                          >  1:5582834/1‑52 (MQ=255)
                                 ttCAAATTGCGGAGCAACAGCCTGCTTCATCGGCACAATATGCTGGTTGCTGt                                                        <  1:937645/53‑1 (MQ=255)
                                 ttCAAATTGCGGAGCAACAGCCTGCTTCATCGGCACAATATGCTGGTTGCTGt                                                        <  1:3300172/53‑1 (MQ=255)
                                  tCAAATTGCGGAGCAACAGCCTGCTTCATCGGCACaa                                                                       >  1:1566426/1‑37 (MQ=255)
                                  tCAAATTGCGGAGCAACAGCCTGCTTCATCGGCACAATATGCTGGTTGCTGTAATCACCGGTCATCGTc                                       >  1:856251/1‑69 (MQ=255)
                                   cAAATTGCGGAGCAACAGCCTGCTTCATCGGCACAATATGc                                                                  >  1:1447457/1‑41 (MQ=255)
                                    aaaTTGCGGAGCAACAGCCTGCTTCATCGGCACAATATGCTGGTTGCTGTAATCACCGGTCATc                                          >  1:1534788/1‑64 (MQ=255)
                                    aaaTTGCGGAGCAACAGCCTGCTTCATCGGCACAATATGCTGGTTGCTGTAATCACCGGTCATCGTCAAGt                                   <  1:3778107/71‑1 (MQ=255)
                                     aaTTGCGGAGCAACAGCCTGCTTCATCGGCACAATATGCTGGTTGCTGTAATCACCGGTCATCGTCAAGTc                                  <  1:2069629/71‑1 (MQ=255)
                                      aTTGCGGAGCAACAGCCTGCTTCATCGGCACAATATGCt                                                                 <  1:4155405/39‑1 (MQ=255)
                                      aTTGCGGAGCAACAGCCTGCTTCATCGGCACAATATGCt                                                                 <  1:3025261/39‑1 (MQ=255)
                                      aTTGCGGAGCAACAGCCTGCTTCATCGGCACAATATGCTGGTTGCt                                                          <  1:4320656/46‑1 (MQ=255)
                                       ttGCGGAGCAACAGCCTGCTTCATCGGCACAATATGCTGGTTGCTGTAAtac                                                   >  1:1033626/1‑50 (MQ=255)
                                       ttGCGGAGCAACAGCCTGCTTCATCGGCACAATATGCTGGTTGCTGTAATCACCGGTCATCGTCAAGTCAt                                >  1:4026285/1‑71 (MQ=255)
                                       ttGCGGAGCAACAGCCTGCTTCATCGGCACAATATGCTGGTTGCTGTAATCACCGGTCATCGTCAAGTCAt                                <  1:5566292/71‑1 (MQ=255)
                                          cGGAGCAACAGCCTGCTTCATCGGCACAATATGCTGGTTGCTGTAATCACCGGTCATCGTCAAGTCATTgc                             >  1:250120/1‑71 (MQ=255)
                                            gAGCAACAGCCTGCTTCATCGGCACAATATGCTGGTTGCTGTAATCACCGGTCATCGTCAAGTCa                                 <  1:2915445/65‑1 (MQ=255)
                                             aGCAACAGCCTGCTTCATCGGCACAATATGCTGGTTGCTGTAATCACCGGTCATCGTCAAGTCATTGCGCt                          >  1:4602458/1‑71 (MQ=255)
                                               cAACAGCCTGCTTCATCGGCACAATATGCTGGTTGCTGTAATCACCGGTCATCGTCAAGTCATTGCGCTc                         >  1:3774467/1‑70 (MQ=255)
                                               cAACAGCCTGCTTCATCGGCACAATATGCTGGTTGCTGTAATCACCGGTCATCGTCAAGTCATTGCGCTc                         >  1:1774422/1‑70 (MQ=255)
                                                 aCAGCCTGCTTCATCGGCACAATATGCTGGTTGCTGTAATCACCGGTCATCTTCAAGTCATTGCGCTCaaa                      >  1:5316869/1‑71 (MQ=255)
                                                 aCAGCCTGCTTCATCGGCACAATATGCTGGTTGCTGTAATCACCGGTCATCGTCAAGTCAtt                               >  1:4889175/1‑62 (MQ=255)
                                                 aCAGCCTGCTTCATCGGCACAATATGCTGGTTGCTGTAATCACCGGTCATCGTCAAGTCATTGCGCTCaaa                      <  1:4148397/71‑1 (MQ=255)
                                                 aCAGCCTGCTTCATCGGCACAATATGCTGGTTGCTGTAATCACCGGTCATCGTCAAGTCATTGCGCTCaaa                      >  1:4710690/1‑71 (MQ=255)
                                                 aCAGCCTGCTTCATAGGCACAATATGCTGGTTGATGt                                                        >  1:5093352/1‑37 (MQ=38)
                                                  cAGCCTGCTTCATCGGCACAATATGCTGGTTGCTGTAATCACCGGTCATCGTCAAGt                                   <  1:195285/57‑1 (MQ=255)
                                                  cAGCCTGCTTCATCGGCACAATATGCTGGTTGCTGTAATCACCGGTCATCGTCAAGt                                   <  1:878753/57‑1 (MQ=255)
                                                  cAGCCTGCTTCATCGGCACAATATGCTGGTTGCTGTAATCACCGGTCATCGTCAAGTCATTGCGCTCAAAc                     >  1:5322952/1‑71 (MQ=255)
                                                  cAGCCTGCTTCATCGGCACAATATGCTGGTTGCTGTAATCACCGGTCATCGTCAAGTCATTGCGCTCAAAc                     <  1:658400/71‑1 (MQ=255)
                                                  cAGCCTGCTTCATCGGCACAATATGCTGGTTGCTGTAATCACCGGTCATCGTCAAGTCATTGCGCTCAAAc                     <  1:1167206/71‑1 (MQ=255)
                                                    gCCTGCTTCATCGGCACAATATGCTGGTTGCTGTAATCACCGGTCATCGTCAAGTCa                                 >  1:909550/1‑57 (MQ=255)
                                                    gCCTGCTTCATCGGCACAATATGCTGGTTGCTGTAATCACCGGTCATCGTCAAGTCa                                 >  1:3182833/1‑57 (MQ=255)
                                                     cttGCTTCATCGGCACCAGATGCTGATTACTGTAATCACCGGTCATGGTGAGATCATTACGCTCAAAAGag                  >  1:4764540/3‑70 (MQ=255)
                                                     cttGCTTCATCGGCACCAGATGCTGATTACTGTAATCACCGGTCATGGTGAGATCATTACGCTCAAAAGag                  >  1:1603803/3‑70 (MQ=255)
                                                     ccTGCTTCATCGGCACAATATGCTGGTTGCTGTAATCACCGGTCATCGTCAAGTCATTGCGCTCaa                       <  1:2712168/66‑1 (MQ=255)
                                                      ttGCTTCATCGGCACCAGATGCTGATTACTGTAAt                                                     >  1:4957641/2‑35 (MQ=19)
                                                      ttGCTTCATCGGCACCAGATGCTGATTACTGTAATCAcc                                                 <  1:418941/38‑1 (MQ=25)
                                                      ttGCTTCATCGGCACCAGATGCTGATTACTGTAATCACCGGTCATGGTGAGATCAtt                               <  1:1105413/56‑1 (MQ=255)
                                                      ttGCTTCATCGGCACCAGATGCTGATTACTGTAATCACCGGTCATGGTGAGATCATTACGCTCaaaag                    <  1:225313/67‑3 (MQ=255)
                                                      ttGCTTCATCGGCACCAGATGCTGAATACTGTAATCACCGGTCATGGTGAGATCATTACGCTCaaaag                    <  1:3971516/67‑3 (MQ=255)
                                                      cTGCTTCATCGGCACAATATGCTGGTTGCTGTAATCACCGGTCATCGTCAAGTCATTGCGCTCAAACGAtg                 <  1:71537/71‑1 (MQ=255)
                                                      cTGCTTCATCGGCACAATATGCTGGTTGCTGTAATCACCGGTCATCGTCAAGTCATTGCGCTCAAACGAtg                 <  1:2590335/71‑1 (MQ=255)
                                                       tGCTTCATCGGCACAATATGCTGGTTGCTGTAATCACCGGTCATCGTCAAGTCATTGCGCTCAAACGAtgt                >  1:1590814/1‑71 (MQ=255)
                                                       tGCTTCATCGGCACAATATGCTGGTTGCTGTAATCACCGGTCATCGTCAAGTCATTGCGCTCAAACGAtgt                >  1:2879637/1‑71 (MQ=255)
                                                       tGCTTCATCGGCACAATATGCTGGTTGCTGTAATCACCGGTCATCGTCAAGTCATTGCCCTCAAACGAtgt                >  1:3636816/1‑71 (MQ=255)
                                                        gCTTCATCGGCACCAGATGCTGATTACTGTAATCACCGGTCATGGTGAGATCATTACGCTCAAAAGagg                 >  1:4307876/1‑67 (MQ=255)
                                                        gCTTCATCGGCACAATATGCTGGTTGCTGTAATCACCGGTCATCGTCAAGTCATTGCGCTCAAACGAtgtg               >  1:5045382/1‑71 (MQ=255)
                                                        gCTTCATCGGCACAATATGCTGGTTGCTGTAATCACCGGTCATCGTCAAGTCATTGCGCTCAAACGAtgtg               >  1:3430096/1‑71 (MQ=255)
                                                         cTTCATCGGCACAATATGCTGGTTGCTGTAATCACCGGTCATCGTCAAGTCATTGCGCTCAAACGAtgtg               <  1:2951810/70‑1 (MQ=255)
                                                         cTTCATCGGCACAATATGCTGGTTGCTGTAATCACCGGTCATCGTCAAGTCATTGCGCTCAAACGATgtgg              <  1:3553840/71‑1 (MQ=255)
                                                          ttCATCGGCACCAGATGCTGATTACTGTAATCACCGGTCATGGTGAGATCAtt                               >  1:3875618/1‑53 (MQ=255)
                                                          ttCATCGGCACCAGATGCTGATTACTGTAATCACCGGTCATGGTGAGATCAtt                               >  1:3026116/1‑53 (MQ=255)
                                                          ttCATCGGCACAATATGCTGGTTGCTGTAATCACCGGTCa                                            >  1:2916854/1‑40 (MQ=255)
                                                          ttCATCGGCACAATATGCTGGTTGCTGTAATCACCGGTCATCGTCAAGTCATTGCGCTCAAAc                     <  1:5655367/63‑1 (MQ=255)
                                                           tCATCGGCACAATATGCTGGTTGCTGTAATCACCGGTCATCGTCAAGTCATTGCGCTCAAACGATgtggt             >  1:3032629/1‑70 (MQ=255)
                                                           tCATCGGCACAATATGCTGGTTGCTGTAATCACCGGTCATCGTCAAGTCATTGCGCTCAAACGATgtggt             >  1:4743670/1‑70 (MQ=255)
                                                            cATCGGCACCAGATGCTGATTACTGTAATCACCGGTCATGGTGAGATCAtta                              >  1:4800512/1‑51 (MQ=255)
                                                            cATCGGCACCAGATGCTGATTACTGTAATCACCGGTCATGGTGAGATCAtta                              >  1:1894571/1‑51 (MQ=255)
                                                            cATCGGCACCAGATGCTGATTACTGTAATCACCGGTCATGGTGAGATCAtta                              >  1:1386202/1‑51 (MQ=255)
                                                            cATCGGCACCAGATGCTGATTACTGTAATCACCGGTCATGGTGAGATCATTACGCTCAAAAGAGgtagtc            <  1:1185271/70‑2 (MQ=255)
                                                             aTCGGCACAATATGCTGGTTGCTGTAATCACCGGTCATCGTCAAGTCATTGCGCTCAAACGATGTGGTGAt          <  1:2179754/71‑1 (MQ=255)
                                                             aTCGGCACAATATGCTGGTTGCTGTAATCACCGGTCATCGTCAAGTCATTGCGCTCAAACGATGTGGTGAt          <  1:3427176/71‑1 (MQ=255)
                                                             aTCGGCACAATATGCTGGTTGCTGTAATCACCCGTCATCGTCAAGTCATTGCGCTCAAACGATGTGGTGAt          <  1:5504730/71‑1 (MQ=255)
                                                              tCGGCACCAGATGCTGATTACTGTAATCACCGGTCATGGTGAGATCATTACGCTCAAAAGAGgtagt             <  1:221067/67‑1 (MQ=255)
                                                              tCGGCACAATATGCTGGTTGCTGTAATCACCGGTCATCGTCAAGTc                                  <  1:186794/46‑1 (MQ=255)
                                                              tCGGCACAATATGCTGGTTGCTGTAATCACCGGTCATCGTCAAGTCATTGCGCTCa                        <  1:4401480/56‑1 (MQ=255)
                                                              tCGGCACAATATGCTGGTTGCTGTAATCACCGGTCATCGTCAAGTCATTGCGCTCa                        <  1:3467363/56‑1 (MQ=255)
                                                              tCGGCACAATATGCTGGTTGCTGTAATCACCGGTCATCGTCAAGTCATTGCGCTCa                        <  1:5094596/56‑1 (MQ=255)
                                                               cGGCACAATATGCTGGTTGCTGTAATCACCGGTCATCGTCAAGTCATTGCGCTCAAACGATGTGGTGATCg        >  1:2755171/1‑71 (MQ=255)
                                                                ggCACCAGATGCTGATTACTGTAATCACCGGTCATGGTGAGATCATTacg                            >  1:1250668/1‑50 (MQ=255)
                                                                ggCACAATATGCTGGTTGCTGTAATCACCGGTCATCg                                         >  1:5523363/1‑37 (MQ=255)
                                                                ggCACAATATGCTGGTTGCTGTAATCACCGGTCATCg                                         >  1:1657379/1‑37 (MQ=255)
                                                                ggCACAATATGCTGGTTGCTGTAATCACCGGTCATCg                                         >  1:5260328/1‑37 (MQ=255)
                                                                ggCACAATATGCTGGTTGCTGTAATCACCGGTCATCGTCAAGTCATTGCGCTCAAACGATGTGGTGATCgg       >  1:523185/1‑71 (MQ=255)
                                                                   acaATATGCTGGTTGCTGTAATCACCGGTCATCGTCAAGTCATTGCGCTCAAACGATGTGGTGATCGGTaa    <  1:4583160/71‑1 (MQ=255)
                                                                    caATATGCTGGTTGCTGTAATCACCGGTCATCGTCAAGTCATTGCGCTCAAACGATGTGGTGATCGGTaa    <  1:490495/70‑1 (MQ=255)
                                                                     aaTATGCTGGTTGCTGTAATCACCGGTCATCGTCAAGTCATTGCGCTCAAACGATGTGGTGATCGGTAATa  <  1:5124843/71‑1 (MQ=255)
                                                                     |                                                                      
AAGATCGGCAAACACGTCAAAATCGTTACGCGCTTCAAATTGCGGAGCAACAGCCTGCTTCATCGGCACAATATGCTGGTTGCTGTAATCACCGGTCATCGTCAAGTCATTGCGCTCAAACGATGTGGTGATCGGTAATA  >  minE/1259280‑1259419

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A