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 835,013 A→G 21.9% A1157A (GCA→GCG) ‡ narG → nitrate reductase 1, alpha subunit

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE835,0130AG21.9% 238.3 / 60.7 123A1157A (GCA→GCG) ‡narGnitrate reductase 1, alpha subunit
Reads supporting (aligned to +/- strand):  ref base A (44/52);  new base G (16/11);  total (60/63)
Fisher's exact test for biased strand distribution p-value = 2.77e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

Only 100 of 131 total aligned reads displayed.

ACTGGATTGAAGTCTTCAACAGCAACGGTGCTCTGACTGCCCGTGCGGTTGTCAGCCAGCGTGTTCCGGCAGGGATGACCATGATGTACCACGCGCAGGAACGTATCGTTAACCTGCCTGGTTCGGAAATTACCCAACAGC  >  minE/834943‑835083
                                                                      |                                                                      
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)
    gATTGAAGTCTTCAACAGCAACGGTGCTCTGACTGCCCGTGCGGTTGTCAGCCAGCGTGTTCCGGCAGGGa                                                                    >  1:3396998/1‑71 (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)
              ttCAACAGCAACGGTGCTCTGACTGCCCGTGCGGTTGTCAGCCAGCGTGTTCCGGCAgg                                                                      <  1:3374290/59‑1 (MQ=255)
              ttCAACAGCAACGGTGCTCTGACTGCCCGTGCGGTTGTCAGCCAGCGTGTTCCGGCAgg                                                                      <  1:828517/59‑1 (MQ=255)
              ttCAACAGCAACGGTGCTCTGACTGCCCGTGCGGTTGTCAGCCAGCGTGTTCCGGCAGGGATGACCatgat                                                          >  1:1140239/1‑71 (MQ=255)
                cAACAGCAACGGTGCTCTGACTGCCCGTGCGGTTGTCAGCCAGCGTGTTCCGGCAGGGAt                                                                   >  1:783057/1‑60 (MQ=255)
                cAACAGCAACGGTGCTCTGACTGCCCGTGCGGTTGTCAGCCAGCGTGTTCCGGCAGGGAt                                                                   >  1:1074713/1‑60 (MQ=255)
                   cAGCAACGGTGCTCTGACTGCCCGTGCGGTTGTCAGCCAGCGTGTTCCGGCAGGGATGACCATGATGTAcc                                                     <  1:3832943/71‑1 (MQ=255)
                    gccAACGGCGCGCTGACTGCCCGCGCGGTGGTCAGCCAACGTGTACCGCCGGGCATGACCATGATGTATCa                                                    >  1:1251324/3‑71 (MQ=255)
                       aaCGGTGCTCTGACTGCCCGTGCGGTTGTCAGCCAGCGTGTTCCGGCAGGGATGACCATGATGTACCAcgc                                                 >  1:1958381/1‑71 (MQ=255)
                       aaCGGTGCTCTGACTGCCCGTGCGGTTGTCAGCCAGCGTGTTCCGGCAGGGATGACCATGATGTACCAcgc                                                 >  1:906405/1‑71 (MQ=255)
                        aCGGTGCTCTGACTGCCCGTGCGGTTGTCAGCCAGCGTGTTCCGGCAg                                                                       <  1:3711934/48‑1 (MQ=255)
                        aCGGCGCGCTGACTGCCCGCGCGGTGGTCAGCCAACGTGTACCGCCGGGCATGACCATGATGTat                                                      >  1:2708417/1‑64 (MQ=255)
                        aCGGCGCGCTGACTGCCCGCGCGGTGGTCAGCCAACGTGTACCGCCGGGCATGACCATGATGTat                                                      >  1:2962100/1‑64 (MQ=255)
                        aCGGCGCGCTGACTGCCCGCGCGGTGGTCAGCCAACGTGTACCGCCGGGCATGACCATGATGTat                                                      >  1:1890195/1‑64 (MQ=255)
                        aCGGCGCGCTGACTGCCCGCGCGGTGGTCAGCCAACGTGTACCGCCGGGCATGACCATGATGTATCAcgcc                                                >  1:3788152/1‑70 (MQ=255)
                         cGGTGCTCTGACTGCCCGTGCGGTTGTCAGCCAGCGTGTTCCGGCAGGGATg                                                                  <  1:2474331/52‑1 (MQ=255)
                            tGCTCTGACTGCCCGTGCGGTTGTCAGCCAGCGTGTTCCGGCAGGGATGACCATGATGTACCACGCGCAgg                                            <  1:859508/71‑1 (MQ=255)
                                ctGACTGCCCGTGCGGTTGTCAGCCAGCGTGTTCCGGCAGGGATGACCATGATGTACCACGCGCAGGAACg                                        >  1:447976/1‑71 (MQ=255)
                                 tGACTGCCCGTGCGGTTGTCAGCCAGCGTGTTTCGGCAGGGATGACCATGATGTACCACGCGCAGGAACg                                        >  1:4915988/1‑70 (MQ=255)
                                  gACTGCCCGTGCGGTTGTCAGGCAGCGTGTTCCGGCAGGGATGACCATGATGTACCACGCGCAGGAACGTa                                      >  1:4388736/1‑71 (MQ=255)
                                  gACTGCCCGTGCGGTTGTCAGCCAGCGTGTTCCGGCAGGGATGACCATGATGTACCACGCGCAGGAACGTa                                      >  1:2540680/1‑71 (MQ=255)
                                   aCTGCCCGCGCGGTGGTCAGCCAACGTGTACCGCCGGGCATGACCATGATGTATCACGCCCAGGAACGCAt                                     >  1:91440/1‑71 (MQ=255)
                                     tGCCCGTGCGGTTGTCAGCCAGCGTGTTCCGGCAGGGATGACCatgatg                                                         <  1:836604/49‑1 (MQ=255)
                                       cccGTGCGGTTGTCAGCCAGCGTGTTCCGGCAGGGATGACCATGATGTACCACGCGCAGGAACGTATCg                                   <  1:661469/69‑1 (MQ=255)
                                       cccGTGCGGTTGTCAGCCAGCGTGTTCCGGCAGGGATGACCATGATGTACCACGCGCAGGAACGTATCGtt                                 <  1:4116101/71‑1 (MQ=255)
                                       cccGTGCGGTTGTCAGCCAGCGTGTTCCGGCAGGGATGACCATGATGTACCACGCGCAGGAACGTATCGt                                  >  1:2246713/1‑70 (MQ=255)
                                       cccGCGCGGTGGTCAACCAACGTGTACCGCCGGGCATGACCATGATGTATCACGCCCAGGAACGCAttat                                  >  1:45183/1‑67 (MQ=255)
                                        ccGTGCGGTTGTCAGCCAGCGTGTTCCGGCAGGGATGACCATGATGTACCACGCGCAGGAACGt                                       <  1:1621651/64‑1 (MQ=255)
                                        ccGTGCGGTTGTCAGCCAGCGTGTTCCGGCAGGGATGACCATGATGTACCACGCGCAGGAACGt                                       <  1:3891855/64‑1 (MQ=255)
                                        ccGTGCGGTTGTCAGCCAGCGTGTTCCGGCAGGGATGACCATGATGTACCACGCGCAGGAACGt                                       <  1:3707454/64‑1 (MQ=255)
                                          gTGCGGTTGTCAGCCAGCGTGTTCCGGCAGGGATGACCATGATGTACCACGCGCAGGAACGTAt                                     <  1:2908133/64‑1 (MQ=255)
                                           tGCGGTTGTCAGCCAGCGTGTTCCGGCAGGGATGACCa                                                              <  1:2461041/38‑1 (MQ=255)
                                           tGCGGTTGTCAGCCAGCGTGTTCCGGCAGGGATGACCATGATGTa                                                       >  1:293482/1‑45 (MQ=255)
                                           tGCGGTTGTCAGCCAGCGTGTTCCGGCAGGGATGACCATGATGTa                                                       >  1:641543/1‑45 (MQ=255)
                                           tGCGGTTGTCAGCCAGCGTGTTCCGGCAGGGATGACCATGATGTa                                                       >  1:1371684/1‑45 (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)
                                             cGGTTGTCAGCCAGCGTGTTCCGGCAGGGATGACCATGATGTACCACGCGCAGGAACGTATCGTTAAcctg                           >  1:4223642/1‑71 (MQ=255)
                                                ttGTCAGCCAGCGTGTTCCGGCAGGGATGACCATGATGTACCACGCGCAGGAACGTATCGTTAAcctgcct                        <  1:2602551/71‑1 (MQ=255)
                                                ttGTCAGCCAGCGTGTTCCGGCAGGGATGACCATGATGTACCACGCGCAGGAACGTATCGTTAAcctgcct                        <  1:1044911/71‑1 (MQ=255)
                                                  gTCAGCCAGCGTGTTCCGGCAGGGATGACCatgatg                                                         >  1:1405320/1‑36 (MQ=255)
                                                  gTCAGCCAGCGTGTTCCGGCAGGGATGACCATGATGTACCACGCGCAGGAACg                                        >  1:1033878/1‑53 (MQ=255)
                                                  gTCAGCCAGCGTGTTCCGGCAGGGATGACCATGATGTACCACGCGCAGGAACGTATCGTTAACCTGCCTgg                      >  1:4585703/1‑71 (MQ=255)
                                                  gTCAGCCAACGTGTACCGCCGGGCATGACCATGATGTATCACGCCCa                                              <  1:2518405/47‑1 (MQ=16)
                                                  gTCAGCCAACGTGTACCGCCGGGCATGACCATGATGTATCACGCCCa                                              <  1:4638057/47‑1 (MQ=16)
                                                  gTCAGCCAACGTGTACCGCCGGGCATGACCATGATGTATCACGCCCa                                              <  1:3277177/47‑1 (MQ=16)
                                                   tCAGCCAGCGTGTTCCGGCAGGGATGACCATGATGTACCACGCGCAGGAACGTATCGtt                                 <  1:745313/59‑1 (MQ=255)
                                                   tCAGCCAACGTGTACCGCCGGGCATGACCATGATGTATCACGCCCAGGAACGCAt                                     <  1:3224699/55‑1 (MQ=255)
                                                    cagccagcGTGTTCCGGCAGGGATGACCATGATGTACCACGCGCAGGAACGTATCGTTAACCTGCCTGGtt                    >  1:4710332/1‑71 (MQ=255)
                                                     agccagcGTGTTCCGGCAGGGATGACCATGATGTACCACGCGCAGGAACGTATCGTTAACCTGCCTGGTTc                   >  1:168575/1‑71 (MQ=255)
                                                     agccagcGTGTTCCGGCAGGGATGACCATGATGTACCACGCGCAGGAACGTATCGTTAACCTGCCTGGTTc                   >  1:2082186/1‑71 (MQ=255)
                                                     agccagcGTGTTCCGGCAGGGATGACCATGATGTACCACGCGCAGGAACGTATCGTTAACCTGCCTGGTTc                   >  1:832669/1‑71 (MQ=255)
                                                     agccaacGTGTACCGCCGGGCATGACCATGATGTATCACGCCCAGGAACGCATTATGAATATTCCTGGTTc                   >  1:3183756/1‑71 (MQ=255)
                                                      gccagcGTGTTCCGGCAGGGATGACCATGATGTACCACGCGCAGGAACGTATCGTTa                                <  1:4065311/57‑1 (MQ=255)
                                                      gccagcGTGTTCCGGCAGGGATGACCATGATGTACCACGCGCAGGAACGTATCGTTa                                <  1:5384197/57‑1 (MQ=255)
                                                      gccagcGTGTTCCGGCAGGGATGACCATGATGTACCACGCGCAGGAACGTATCGTTa                                <  1:2997136/57‑1 (MQ=255)
                                                       ccagcGTGTTCCGGCAGGGATGACCATGATGTACCACGCGCAGGAACGTATCGTTAACCTGCCTGGTTCgg                 <  1:4492449/71‑1 (MQ=255)
                                                       ccagcGTGTTCCGGCAGGGATGACCATGATGTACCACGCGCAGGAACGTATCGTTAACCTGCCTGGTTCgg                 <  1:641250/71‑1 (MQ=255)
                                                       ccaacGTGTACCGCCGGGCATGACCATGATGTATCACGCCCAGGAACGCATTATGAATATTCCTGGTTCgg                 <  1:3500068/71‑1 (MQ=255)
                                                         agcGTGTTCCGGCAGGGATGACCATGATGTACCACGCGCAGGAACGTATCGTTAACCTGCCTGGTTCGGa                >  1:1111952/1‑70 (MQ=255)
                                                         agcGTGTTCCGGCAGGGATGACCATGATGTACCACGCGCAGGAACGTATCGTTAACCTGCCTGGTTCGGa                <  1:5320507/70‑1 (MQ=255)
                                                         aacGTGTACCGCCGGGCATGACCATGATGTATCACGCCCAgg                                            <  1:442422/40‑1 (MQ=12)
                                                         aacGTGTACCGCCGGGCATGACCATGATGTATCACGCCCAGGAACGCATTATGAATATTCCTGGTTCg                  <  1:1771948/66‑1 (MQ=255)
                                                           cGTGTTCCGGCAGGGATGACCATGATGTACCACGCGCAGGAACGTATCGTTAACCTGCCTGGTTCgg                 <  1:3043868/67‑1 (MQ=255)
                                                           cGTGTTCCGGCAGGGATGACCATGATGTACCACGCGCAGGAACGTATCGTTAACCTGCCTGGTTCgg                 <  1:2805172/67‑1 (MQ=255)
                                                           cGTGTTCCGGCAGGGATGACCATGATGTACCACGCGCAGGAACGTATCGTTAACCTGCCTGGTTCgg                 <  1:5510869/67‑1 (MQ=255)
                                                            gtgtACCGCCGGGCATGACCATGATGTATCACGCCCAGGAACGCATTATGAATATTCCTGGTTCGGaagta            <  1:4552860/71‑4 (MQ=255)
                                                            gtgtACCGCCGGGCATGACCATGATGTATCACGCCCAGGAACGCATTATGAATATTCCTGGTTCGGaagt             >  1:540723/1‑68 (MQ=255)
                                                             tgtTCCGGCAGGGATGACCATGATGTACCACGCGCAGGAACGTATCGt                                  <  1:4901642/48‑1 (MQ=255)
                                                             tgtTCCGGCAGGGATGACCATGATGTACCACGCGCAGGAACGTATCGt                                  <  1:5269924/48‑1 (MQ=255)
                                                             tgtTCCGGCAGGGATGACCATGATGTACCACGCGCAGGAACGTATCGt                                  <  1:4029514/48‑1 (MQ=255)
                                                               ttCCGGCAGGGATGACCATGATGTACCACGCGCAg                                             >  1:5210523/1‑35 (MQ=255)
                                                               ttCCGGCAGGGATGACCATGATGTACCACGCGCAGGAACGTATCGTTAACCTGCCTGGTTCGGAAATTAcc         >  1:3714975/1‑71 (MQ=255)
                                                                 ccGGCAGGGATGACCATGATGTACCACGCGCAGGAACGTATCGTTAACCTGCCTGGTTCGGAAATTAccc        <  1:266157/70‑1 (MQ=255)
                                                                 ccGGCAGGGATGACCATGATGTACCACGCGCAGGAACGTATCGTTAACCTGCCTGGTTCGGAAATTAccc        >  1:5149989/1‑70 (MQ=255)
                                                                 ccGGCAGGGATGACCATGATGTACCACGCGCAGGAACGTATCGTTAACCTGCCTGGTTCGGAAATTAccc        >  1:1956105/1‑70 (MQ=255)
                                                                  cGGCAGGGATGACCATGATGTACCACGCGCAGGAACGTATCGTTAACCTGCCTGGTTCGGAAATTACCCaa      <  1:100192/71‑1 (MQ=255)
                                                                  cGGCAGGGATGACCATGATGTACCACGCGCAGGAACGTATCGTTAACCTGCCTGGTTCGGAAATTACCCa       <  1:2256105/70‑1 (MQ=255)
                                                                     cAGGGATGACCATGATGTACCACGCGCAGGAACGTATCGTTAACCTGCCTGGTTCGGAAATTACCCAACAg   <  1:5439251/71‑1 (MQ=255)
                                                                      aGGGATGACCATGATGTACCACGCGCAGGAACGTATCGTTAACCTGCCTGGTTCGGAAATTACCCAACAGc  <  1:711814/71‑1 (MQ=255)
                                                                      aGGGATGACCATGATGTACCACGCGCAGGAACGTATCGTTAACCTGCCTGGTTCGGAAATTACCCAACAGc  >  1:5220430/1‑71 (MQ=255)
                                                                      aGGGATGACCATGATGTACCACGCGCAGGAACGTATCGTTAACCTGCCTGGTTCGGAAATTACCCAACAGc  >  1:2105595/1‑71 (MQ=255)
                                                                      aGGGATGACCATGATGTACCACGCGCAGGAACGTATCGTTAACCTGCCTGGTTCGGAAATTACCCAACAGc  <  1:4290125/71‑1 (MQ=255)
                                                                      aGGGATGACCATGATGTACCACGCGCAGGAACGTATCGTTAACCTGCCTGGTTCGGAAATTACCCAACAGc  <  1:3324322/71‑1 (MQ=255)
                                                                      |                                                                      
ACTGGATTGAAGTCTTCAACAGCAACGGTGCTCTGACTGCCCGTGCGGTTGTCAGCCAGCGTGTTCCGGCAGGGATGACCATGATGTACCACGCGCAGGAACGTATCGTTAACCTGCCTGGTTCGGAAATTACCCAACAGC  >  minE/834943‑835083

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