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 835,007 T→A 23.7% V1155V (GTT→GTA)  narG → nitrate reductase 1, alpha subunit

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE835,0070TA23.7% 241.7 / 70.1 118V1155V (GTT→GTA) narGnitrate reductase 1, alpha subunit
Reads supporting (aligned to +/- strand):  ref base T (39/51);  new base A (17/11);  total (56/62)
Fisher's exact test for biased strand distribution p-value = 1.31e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

Only 100 of 122 total aligned reads displayed.

ATAACGACTGGATTGAAGTCTTCAACAGCAACGGTGCTCTGACTGCCCGTGCGGTTGTCAGCCAGCGTGTTCCGGCAGGGATGACCATGATGTACCACGCGCAGGAACGTATCGTTAACCTGCCTGGTTCGGAAATTACC  >  minE/834937‑835076
                                                                      |                                                                     
aTAACGACTGGATTGAAGTCTTCAACAGCAACGGTGCTCTGACTGCCCGTGCGGTTGTCAGCCAGCGTGtt                                                                       >  1:1871631/1‑71 (MQ=255)
 tAACGACTGGATTGAAGTCTTCAACAGCAACGGTGCTCTGACTGCCCGTGCGGTTGTCAGCCAGCGTGTTc                                                                      <  1:4348712/71‑1 (MQ=255)
  aaCGACTGGGTGGAAGTATTCAACGCCAACGGCGCGCTGACTGCCCGCGCGGTGGTCAGCCAACGTGTAcc                                                                     >  1:5064802/1‑71 (MQ=255)
  aaCGACTGGATTGAAGTCTTCAACAGCAACGGTGCTCTGACTGCCCGTGCGGTTGTCAGCCAGCGTGTTcc                                                                     >  1:4115595/1‑71 (MQ=255)
  aaCGACTGGATTGAAGTCTTCAACAGCAACGGTGCTCTGACTGCCCGTGCGGTTGTCAGCCAGCGTGTTcc                                                                     >  1:4437493/1‑71 (MQ=255)
     gACTGGATTGAAGTCTTCAACAGCAACGGTGCTCTGACTGCCCGTGCGGTTGTCAGCCAGCGTGTTCCGGc                                                                  <  1:3507533/71‑1 (MQ=255)
      aCTGGATTGAAGTCTTCAACAGAAACGGTGCTCTGACTGCCCGTGCGGTTGTCAGCCAGCGTGTTCCGGCa                                                                 <  1:4126060/71‑1 (MQ=255)
       cTGGATTGAAGTCTTCAACAGCAACGGTGCTCTGACTGCCCGTGCGGTTGTCAGCCAGCGTGTTCCGGCAg                                                                >  1:1206532/1‑71 (MQ=255)
          gATTGAAGTCTTCAACAGCAACGGTGCTCTGACTGCCCGTGCGGTTGTCAGCCAGCGTGTTCCGGCAgg                                                               <  1:234117/69‑1 (MQ=255)
          gATTGAAGTCTTCAACAGCAACGGTGCTCTGACTGCCCGTGCGGTTGTCAGCCAGCGTGTTCCGGCAgg                                                               <  1:3777645/69‑1 (MQ=255)
          gATTGAAGTCTTCAACAGCAACGGTGCTCTGACTGCCCGTGCGGTTGTCAGCCAGCGTGTTCCGGCAgg                                                               <  1:4414455/69‑1 (MQ=255)
          gATTGAAGTCTTCAACAGCAACGGTGCTCTGACTGCCCGTGCGGTTGTCAGCCAGCGTGTTCCGGCAgg                                                               <  1:4852113/69‑1 (MQ=255)
          gATTGAAGTCTTCAACAGCAACGGTGCTCTGACTGCCCGTGCGGTTGTCAGCCAGCGTGTTCCGGCAgg                                                               <  1:1166388/69‑1 (MQ=255)
          gATTGAAGTCTTCAACAGCAACGGTGCTCTGACTGCCCGTGCGGTTGTCAGCCAGCGTGTTCCGGCAGGGa                                                             >  1:3396998/1‑71 (MQ=255)
          gATTGAAGTCTTCAACAGCAACGGTGCTCTGACTGCCCGTGCGGTTGTCAGCCAGCGTGTTCCGGCAGGGa                                                             >  1:5364934/1‑71 (MQ=255)
              gAAGTATTCAACGCCAACGGCGCGCTGACTGCCCGCGCGGTGGTCAGCCAACGTGTACCGCCGGGCATGAc                                                         >  1:2012149/1‑71 (MQ=255)
               aaGTCTTCAACAGCAACGGTGCTCTGACTGCCCGTGCGGTTGTCAGCCAGCGTGTTCCGGCAGGGATGAc                                                         <  1:388643/70‑1 (MQ=255)
                aGTCTTCAACAGCAACGGTGCTCTGACTGCCCGTGCGGTTGTCAGCCAGCGTGTTCCGGCAGGGATGa                                                          >  1:1540180/1‑68 (MQ=255)
                aGTCTTCAACAGCAACGGTGCTCTGACTGCCCGTGCGGTTGTCAGCCAGCGTGTTCCGGCAGGGATGACCa                                                       <  1:5112215/71‑1 (MQ=255)
                aGTCTTCAACAGCAACGGTGCTCTGACTGCCCGTGCGGTTGTCAGCCAGCGTGTTCCGGCAGGGATGACCa                                                       <  1:114199/71‑1 (MQ=255)
                 gtattCAACGCCAACGGCGCGCTGACTGCCCGCGCGGTGGTCAGCCAACGTGTACCGCCGGGCATGACCa                                                       >  1:4559720/4‑70 (MQ=255)
                 gTCTTCAACAGCAACGGTGCTCTGACTGCCCGTGCGGTTGTCAGCCAGCGTGTTCCGGCAGGGATGACCat                                                      >  1:1337076/1‑71 (MQ=255)
                 gTCTTCAACAGCAACGGTGCTCTGACTGCCCGTGCGGTTGTCAGCCAGCGTGTTCCGGCAGGGATGACCat                                                      >  1:4921961/1‑71 (MQ=255)
                 gTCTTCAACAGCAACGGTGCTCTGACTGCCCGTGCGGTTGTCAGCCAGCGTGTTCCGGCAGGGATGACCat                                                      >  1:4671006/1‑71 (MQ=255)
                 gTCTTCAACAGCAACGGTGCTCTGACTGCCCGTGCGGTTGTCAGCCAGCGTGTTCCGGCAGGGATGACCat                                                      >  1:277424/1‑71 (MQ=255)
                    ttCAACAGCAACGGTGCTCTGACTGCCCGTGCGGTTGTCAGCCAGCGTGTTCCGGCAgg                                                               <  1:3374290/59‑1 (MQ=255)
                    ttCAACAGCAACGGTGCTCTGACTGCCCGTGCGGTTGTCAGCCAGCGTGTTCCGGCAgg                                                               <  1:828517/59‑1 (MQ=255)
                      cAACAGCAACGGTGCTCTGACTGCCCGTGCGGTTGTCAGCCAGCGTGTTCCGGCAGGGAt                                                            >  1:1074713/1‑60 (MQ=255)
                      cAACAGCAACGGTGCTCTGACTGCCCGTGCGGTTGTCAGCCAGCGTGTTCCGGCAGGGAt                                                            >  1:783057/1‑60 (MQ=255)
                         cAGCAACGGTGCTCTGACTGCCCGTGCGGTTGTCAGCCAGCGTGTTCCGGCAGGGATGACCATGATGTAcc                                              <  1:3832943/71‑1 (MQ=255)
                          gccAACGGCGCGCTGACTGCCCGCGCGGTGGTCAGCCAACGTGTACCGCCGGGCATGACCATGATGTATCa                                             >  1:1251324/3‑71 (MQ=255)
                           ccAACGGCGCGCTGACTGCCCGCGCGGTGGTCAGCCAACGTGTACCGCCGGGCATGACCATGATGTATCAc                                            >  1:4609626/2‑71 (MQ=255)
                             aaCGGTGCTCTGACTGCCCGTGCGGTTGTCAGCCAGCGTGTTCCGGCAGGGATGACCATGATGTACCAcgc                                          >  1:906405/1‑71 (MQ=255)
                             aaCGGCGCGCTGACTGCCCGCGCGGTGGTCAGCCAACGTGTACCGCCGGGCATGACCATGATGTATCAcgc                                          >  1:828027/1‑71 (MQ=255)
                              aCGGTGCTCTGACTGCCCGTGCGGTTGTCAGCCAGCGTGTTCCGGCAg                                                                <  1:3711934/48‑1 (MQ=255)
                              aCGGCGCGCTGACTGCCCGCGCGGTGGTCAGCCAACGTGTACCGCCGGGCATGACCATGATGTat                                               >  1:2962100/1‑64 (MQ=255)
                              aCGGCGCGCTGACTGCCCGCGCGGTGGTCAGCCAACGTGTACCGCCGGGCATGACCATGATGTat                                               >  1:2708417/1‑64 (MQ=255)
                              aCGGCGCGCTGACTGCCCGCGCGGTGGTCAGCCAACGTGTACCGCCGGGCATGACCATGATGTat                                               >  1:1890195/1‑64 (MQ=255)
                              aCGGCGCGCTGACTGCCCGCGCGGTGGTCAGCCAACGTGTACCGCCGGGCATGACCATGATGTATCAcgcc                                         >  1:3788152/1‑70 (MQ=255)
                               cGGTGCTCTGACTGCCCGTGCGGTTGTCAGCCAGCGTGTTCCGGCAGGGATg                                                           <  1:2474331/52‑1 (MQ=255)
                                ggTGCTCTGACTGCCCGTGCGGTTGTCAGCCAGCGTGTTCCGGCAGGGATGACCATGATGTACCAcgcg                                         >  1:4350576/1‑69 (MQ=255)
                                  tGCTCTGACTGCCCGTGCGGTTGTCAGCCAGCGTGTTCCGGCAGGGATGACCATGATGTACCACGCGCAgg                                     <  1:859508/71‑1 (MQ=255)
                                    cgctGACTGCCCGCGCGGTGGTCAGCCAACGTGTACCGCCGGGCATGACCATGATGTATCACGCCCAGGaa                                   <  1:412202/69‑1 (MQ=255)
                                     tctGACTGCCCGTGCGGTTGTCAGCCAGCGTGTTCCGGc                                                                  <  1:5557475/39‑1 (MQ=255)
                                      ctGACTGCCCGTGCGGTTGTCAGCCAGCGTGTTCCGGCAGGGATGACCATGATGTACCACGCGCAGGAACg                                 >  1:447976/1‑71 (MQ=255)
                                        gACTGCCCGTGCGGTTGTCAGGCAGCGTGTTCCGGCAGGGATGACCATGATGTACCACGCGCAGGAACGTa                               >  1:4388736/1‑71 (MQ=255)
                                         aCTGCCCGCGCGGTGGTCAGCCAACGTGTACCGCCGGGCATGACCATGATGTATCACGCCCAGGAACGCAt                              >  1:91440/1‑71 (MQ=255)
                                           tGCCCGTGCGGTTGTCAGCCAGCGTGTTCCGGCAGGGATGACCatgatg                                                  <  1:1829981/49‑1 (MQ=255)
                                             cccGTGCGGTTGTCAGCCAGCGTGTTCCGGCAGGGATGACCATGATGTACCACGCGCAGGAACGTATCg                            <  1:661469/69‑1 (MQ=255)
                                             cccGTGCGGTTGTCAGCCAGCGTGTTCCGGCAGGGATGACCATGATGTACCACGCGCAGGAACGTATCGtt                          <  1:4116101/71‑1 (MQ=255)
                                             cccGCGCGGTGGTCAACCAACGTGTACCGCCGGGCATGACCATGATGTATCACGCCCAGGAACGCAttat                           >  1:45183/1‑67 (MQ=255)
                                              ccGTGCGGTTGTCAGCCAGCGTGTTCCGGCAGGGATGACCATGATGTACCACGCGCAGGAACGt                                <  1:3707454/64‑1 (MQ=255)
                                              ccGTGCGGTTGTCAGCCAGCGTGTTCCGGCAGGGATGACCATGATGTACCACGCGCAGGAACGt                                <  1:3891855/64‑1 (MQ=255)
                                                gTGCGGTTGTCAGCCAGCGTGTTCCGGCAGGGATGACCATGATGTACCACGCGCAGGAACGTAt                              <  1:2908133/64‑1 (MQ=255)
                                                 tGCGGTTGTCAGCCAGCGTGTTCCGGCAGGGATGACCa                                                       <  1:2461041/38‑1 (MQ=255)
                                                 tGCGGTTGTCAGCCAGCGTGTTCCGGCAGGGATGACCa                                                       <  1:2566865/38‑1 (MQ=255)
                                                 tGCGGTTGTCAGCCAGCGTGTTCCGGCAGGGATGACCATGATGTa                                                >  1:641543/1‑45 (MQ=255)
                                                 tGCGGTTGTCAGCCAGCGTGTTCCGGCAGGGATGACCATGATGTa                                                >  1:293482/1‑45 (MQ=255)
                                                 tGCGGTTGTCAGCCAGCGTGTTCCGGCAGGGATGACCATGATGTa                                                >  1:1371684/1‑45 (MQ=255)
                                                 tGCGGTTGTCAGCCAGCGTGTTCCGGCAGGGATGACCATGATGTa                                                >  1:1104819/1‑45 (MQ=255)
                                                 tGCGGTTGTCAGCCAGCGTGTTCCGGCAGGGATGACCATGATGTACCACGCGCAGGAACGTATCGtt                          <  1:3040612/67‑1 (MQ=255)
                                                 tGCGGTTGTCAGCCAGCGTGTTCCGGCAGGGATGACCATGATGTACCACGCGCAGGAACGTATCGtt                          <  1:2860641/67‑1 (MQ=255)
                                                 tGCGGTTGTCAGCCAGCGTGTTCCGGCAGGGATGACCATGATGTACCACGCGCAGGAACGTATCGTTAAcc                      >  1:2168996/1‑71 (MQ=255)
                                                  gCGGTTGTCAGCCAGCGTGTTCCGGCAGGGATGACCATGATGTACCACGCGCAGGAACGTATCGTTAAcct                     >  1:1216563/1‑71 (MQ=255)
                                                   cGGTTGTCAGCCAGCGTGTTCCGGCAGGGATGACCATGATGTACCACGCGCAGGAACGTATCGTTAAcctg                    >  1:3045363/1‑71 (MQ=255)
                                                     gTTGTCAGCCAGCGTGTTCCGGCAGGGATGACCATGATGTAc                                               <  1:4478773/42‑1 (MQ=255)
                                                      ttGTCAGCCAGCGTGTTCCGGCAGGGATGACCATGATGTACCACGCGCAGGAACGTATCGTTAAcctgcct                 <  1:2602551/71‑1 (MQ=255)
                                                      ttGTCAGCCAGCGTGTTCCGGCAGGGATGACCATGATGTACCACGCGCAGGAACGTATCGTTAAcctgcct                 <  1:1044911/71‑1 (MQ=255)
                                                      ttGTCAGCCAGCGTGTTCCGGCAGGGATGACCATGATGTACCACGCGCAGGAACGTATCGTTAAcctgcct                 <  1:3365965/71‑1 (MQ=255)
                                                        gTCAGCCAGCGTGTTCCGGCAGGGATGACCatgatg                                                  >  1:1405320/1‑36 (MQ=255)
                                                        gTCAGCCAGCGTGTTCCGGCAGGGATGACCATGATGTACCACGCGCAGGAACg                                 >  1:1033878/1‑53 (MQ=255)
                                                        gTCAGCCAGCGTGTTCCGGCAGGGATGACCATGATGTACCACGCGCAGGAACGTATCGTTAACCTGCCTgg               >  1:4585703/1‑71 (MQ=255)
                                                        gTCAGCCAACGTGTACCGCCGGGCATGACCATGATGTATCACGCCCa                                       <  1:3277177/47‑1 (MQ=16)
                                                        gTCAGCCAACGTGTACCGCCGGGCATGACCATGATGTATCACGCCCa                                       <  1:2518405/47‑1 (MQ=16)
                                                         tCAGCCAGCGTGTTCCGGCAGGGATGACCATGATGTACCACGCGCAGGAACGTATCGtt                          <  1:745313/59‑1 (MQ=255)
                                                         tCAGCCAACGTGTACCGCCGGGCATGACCATGATGTATCACGCCCAGGAACGCAt                              <  1:3224699/55‑1 (MQ=255)
                                                          cagccagcGTGTTCCGGCAGGGATGACCATGATGTACCACGCGCAGGAACGTATCGTTAACCTGCCTGGtt             >  1:4710332/1‑71 (MQ=255)
                                                          cagccaacGTGTACCGCCGGGCATGACCATGATGTATCACGCCCAgg                                     >  1:2456129/1‑47 (MQ=16)
                                                           agccagcGTGTTCCGGCAGGGATGACCATGATGTACCACGCGCAGGAACGTATCGTTAACCTGCCTGGTTc            >  1:839341/1‑71 (MQ=255)
                                                           agccagcGTGTTCCGGCAGGGATGACCATGATGTACCACGCGCAGGAACGTATCGTTAACCTGCCTGGTTc            >  1:832669/1‑71 (MQ=255)
                                                           agccagcGTGTTCCGGCAGGGATGACCATGATGTACCACGCGCAGGAACGTATCGTTAACCTGCCTGGTTc            >  1:2082186/1‑71 (MQ=255)
                                                           agccagcGTGTTCCGGCAGGGATGACCATGATGTACCACGCGCAGGAACGTATCGTTAACCTGCCTGGTTc            >  1:168575/1‑71 (MQ=255)
                                                            gccagcGTGTTCCGGCAGGGATGACCATGATGTACCACGCGCAGGAACGTATCGTTa                         <  1:5384197/57‑1 (MQ=255)
                                                            gccagcGTGTTCCGGCAGGGATGACCATGATGTACCACGCGCAGGAACGTATCGTTa                         <  1:4065311/57‑1 (MQ=255)
                                                            gccagcGTGTTCCGGCAGGGATGACCATGATGTACCACGCGCAGGAACGTATCGTTa                         <  1:2997136/57‑1 (MQ=255)
                                                             ccagcGTGTTCCGGCAGGGATGACCATGATGTACCACGCGCAGGAACGTATCGTTAACCTGCCTGGTTCgg          <  1:641250/71‑1 (MQ=255)
                                                             ccagcGTGTTCCGGCAGGGATGACCATGATGTACCACGCGCAGGAACGTATCGTTAACCTGCCTGGTTCgg          <  1:4492449/71‑1 (MQ=255)
                                                             ccagcGTGTTCCGGCAGGGATGACCATGATGTACCACGCGCAGGAACGTATCGTTAACCTGCCTGCTTCgg          <  1:2188890/71‑1 (MQ=255)
                                                               agcGTGTTCCGGCAGGGATGACCATGATGTACCACGCGCAGGAACGTATCGTTAACCTGCCTGGTTCGGa         <  1:5320507/70‑1 (MQ=255)
                                                               agcGTGTTCCGGCAGGGATGACCATGATGTACCACGCGCAGGAACGTATCGTTAACCTGCCTGGTTCGGa         >  1:1111952/1‑70 (MQ=255)
                                                               aacGTGTACCGCCGGGCATGACCATGATGTATCACGCCCAGGAACGCATTATGAATATTCCTGGTTCg           <  1:1771948/66‑1 (MQ=255)
                                                                acGTGTACCGCCGGGCATGACCATGATGTATCACGCCCAGGaa                                   >  1:4853511/2‑43 (MQ=12)
                                                                 cGTGTTCCGGCAGGGATGACCATGATGTACCACGCGCAGGAACGTATCGTTAACCTGCCTGGTTCgg          <  1:3043868/67‑1 (MQ=255)
                                                                  gtgtACCGCCGGGCATGACCATGATGTATCACGCCCAGGAACGCATTATGAATATTCCTGGTTCGGaagta     <  1:4552860/71‑4 (MQ=255)
                                                                  gtgtACCGCCGGGCATGACCATGATGTATCACGCCCAGGAACGCATTATGAATATTCCTGGTTCGGaagt      >  1:540723/1‑68 (MQ=255)
                                                                   tgtTCCGGCAGGGATGACCATGATGTACCACGCGCAGGAACGTATCGt                           <  1:5269924/48‑1 (MQ=255)
                                                                   tgtTCCGGCAGGGATGACCATGATGTACCACGCGCAGGAACGTATCGt                           <  1:4901642/48‑1 (MQ=255)
                                                                     ttCCGGCAGGGATGACCATGATGTACCACGCGCAg                                      >  1:5210523/1‑35 (MQ=255)
                                                                     ttCCGGCAGGGATGACCATGATGTACCACGCGCAGGAACGTATCGTTAACCTGCCTGGTTCGGa         <  1:3109862/64‑1 (MQ=255)
                                                                     ttCCGGCAGGGATGACCATGATGTACCACGCGCAGGAACGTATCGTTAACCTGCCTGGTTCGGAAATTAcc  >  1:3714975/1‑71 (MQ=255)
                                                                      |                                                                     
ATAACGACTGGATTGAAGTCTTCAACAGCAACGGTGCTCTGACTGCCCGTGCGGTTGTCAGCCAGCGTGTTCCGGCAGGGATGACCATGATGTACCACGCGCAGGAACGTATCGTTAACCTGCCTGGTTCGGAAATTACC  >  minE/834937‑835076

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A