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
A12 F133 I1 R1 102 83.9 4092546 96.1% 3932936 99.9

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 4,627,706 T→G F131C (TTT→TGT)  nadR → trifunctional protein: nicotinamide mononucleotide adenylyltransferase, ribosylnicotinamide kinase, transcriptional repressor

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009134,627,7060TG97.3% 257.0 / ‑0.8 73F131C (TTT→TGT) nadRtrifunctional protein: nicotinamide mononucleotide adenylyltransferase, ribosylnicotinamide kinase, transcriptional repressor
Reads supporting (aligned to +/- strand):  ref base T (1/1);  new base G (36/35);  total (37/36)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.00e-01

GGTTTTGACGATACCCGTGACCGCGCGTTGTTCGAAGACAGTGCCATGTCGCAGCAGCCGACCGTGCCGGATCGTCTGCGTTGGTTATTGCAAACTTTTAAATATCAGAAAAATATTCGCATTCATGCTTTCAACGAAGAGGGCATGGAGCCGTATCCGCACGGCTGGGATGTGTGGAGCAACGGCATCAAAAA  >  NC_000913/4627609‑4627802
                                                                                                 |                                                                                                
ggTTTTGACGATACCCGTGACCGCGCGTTGTTCGAAGACAGTGCCATGTCGCAGCAGCCGACCGTGCCGGATCGTCTGCGTTGGTTATTGCAAACTTGTa                                                                                                <  2:735462/100‑1 (MQ=255)
    ttGACGATACCCGTGACCGCGCGTTGTTCGAAGACAGTGCCATGTCGCAGCAGCCGACCGTGCCGGATCGTCTGCGTTGGTTATTGCAAACTTGTAAata                                                                                            >  1:278492/1‑100 (MQ=255)
    ttGACGATACCCGTGACCGCGCGTTGTTCGAAGACAGTGCCATGTCGCAGCAGCCGACCGTGCCGGATCGTCTGCGTTGGTTATTGCAAACTTGTAAata                                                                                            >  1:1304393/1‑100 (MQ=255)
     tGACGATACCCGAGACCGCGCGTTGTTCGAAGACAGTGCCATGTCGCAGCAGCCGACCGTGCCGGATCGTCTGCGTTGGTTATTGCAAACTTGTAAatat                                                                                           >  1:1344961/1‑100 (MQ=255)
       aCGATACCCGTGACCGCGCGTTGTTCGAAGACAGTGCCATGTCGCAGCAGCCGACCGTGCCGGATCGTCTGCGTTGGTTATTGCAAACTTGTAAATATCa                                                                                         >  2:833159/1‑100 (MQ=255)
          aTACCCGTGACCGCGCGTTGTTCGAAGACAGTGCCATGTCGCAGCAGCCGACCGTGCCGGATCGTCTGCGTTGGTTATTGCAAACTTGTAAATATCAGaa                                                                                      <  1:784657/100‑1 (MQ=255)
            aCCCGTGACCGCGCGTTGTTCGAAGACAGTGCCATGTCGCAGCAGCCGACCGTGCCGGATCGTCTGCGTTGGTTATTGCAAACTTGTAAATATCAGaaaa                                                                                    >  1:615625/1‑100 (MQ=255)
             cccGTGACCGCGCGTTGTTCGAAGACAGTGCCATGTCGCAGCAGCCGACCGTGCCGGATCGTCTGCGTTGGTTATTGCAAACTTGTAAATATCAGaaaaa                                                                                   <  1:196575/100‑1 (MQ=255)
               cGTGACCGCGCGTTGTTCGAAGACAGTGCCATGTCGCAGCAGCCGACCGTGCCGGATCGTCAGCGTTGGTTATTGCAAACTTGTAAATATCAGAAAAata                                                                                 <  2:1259810/100‑1 (MQ=255)
                  gACCGCGCGTTGTTCGAAGACAGTGCCATGTCGCAGCAGCCGACCGTGCCGGATCGTCTGCGTTGGTTATTGCAAACTTGTAAATATCAGAAAAATATTc                                                                              <  1:769902/100‑1 (MQ=255)
                   aCCGCGCGTTGTTCGAAGACGGTGCCATGTCGCAGCAGCCGACCGTGCCGGATCGTCTGCGTTGGTTATTGCAAACTTGTAAAAATAAGAAAAATATTc                                                                              <  2:596595/99‑1 (MQ=255)
                   aCCGCGCGTTGTTCGAAGACAGTGCCATGTCGCAGCAGCCGACCGTGCCGGATCGTCTGCGTTGGTTATTGCAAACTTGTAAATATCAGAAAAATATTCg                                                                             >  1:1414172/1‑100 (MQ=255)
                   aCCGCGCGTTATTCGAAGACAGTGCCATGTCGCAGCAGCCGACCGTGCCGGATCGTCTGCGTTGGTCATCGCAAACTTGTAAATATCAGAAAAATATTCg                                                                             <  2:1344952/100‑1 (MQ=255)
                    ncgcgcgTTGTTCGAAGACAGTGCCATGTCGCAGCAGCCGACCGTGCCGGATCGTCTGCGTTGGTTATTGCAAACTTGTAAATATCAGAAAAATATTCGc                                                                            >  2:1876867/2‑100 (MQ=255)
                    ccGCGCGTTGTTCGAAGACAGTGCCATGTCGCAGCAGCCGACCGTGCCGGATCGTCTGCGTTGGTTATTGCAAACTTGTAAATATCAGAAAAATATTCGc                                                                            <  2:1987514/100‑1 (MQ=255)
                    ccGCGCGTTGTTCAAAGACAGTGCCATGTCGCAGCAGCCGACCGTGCCGGATCGTCTGCGTTGGTTATTGCAAACTTGTAAATATCAGAAAAATATTCGc                                                                            >  2:1265900/1‑100 (MQ=255)
                     cgcgcgTTGTTCGAAGACAGTGCCATGTCGCAGCAGCCGACCGTGCCGGATCGTCTGCGTTGGTTATTGCAAACTTGTAAATATCAGAAAAATATTCGCa                                                                           >  1:328553/1‑100 (MQ=255)
                     cgcgcgTTGTTCGAAGACAGTGCCATGTCGCAGCAGCCGACCGTGCCGGATCGTCTGCGTTGGTTATTGCAAACTTGTAAATATCAGAAAAATATTCGCa                                                                           <  1:1579187/100‑1 (MQ=255)
                      gcgcgTTGTTCGAAGACAGTGCCATGTCGCAGCAGCCGACCGTGCCGGATCGTCTGCGTTGGTTATTGCAAACTTGTAAATATCAGAAAAATATTCGCAt                                                                          <  1:1517132/100‑1 (MQ=255)
                       cgcgTTGTTCGAAGACAGTGCCATGTCGCAGCAGCCGACCGTGCCGGATCGTCTGCGTTGGTTATTGCAAACTTGTAAATATCAGAAAAATATTCGCAtt                                                                         >  1:1712461/1‑100 (MQ=255)
                        gcgTTGTTCGAAGACAGTGCCATGTCGCAGCAGCCGACCGTGCCGGATCGTCTGCGTTGGTTATTGCAAACTTGTAAATATCAGAAAAATATTCGCATTc                                                                        <  2:977533/100‑1 (MQ=255)
                            tgttCGAAGACAGTGCCATGTCGCAGCAGCCGACCGTGCCGGATCGTCTGCGTTGGTTATTGCAAACTTGTAAATATCAGAAAAATATTCGCATTCATGc                                                                    >  2:1972106/1‑100 (MQ=255)
                            tgttCGAAGACAGTGCCATGTCGCAGCAGCCGACCGTGCCGGATCGTCTGCGTTGGTTATTGCAAACTTGTAAATATCAGAAAAATATTCGCATTCATGc                                                                    >  1:897031/1‑100 (MQ=255)
                             gttCGAAGACAGTGCCATGTCGCAGCAGCCGACCGTGCCGGATCGTCTGCGTTGGTTATTGCAAACTTGTAAATATCAGAAGAATATTCGCATTCATGCt                                                                   >  1:1193392/1‑100 (MQ=255)
                             gttCGAAGACAGTGCCATGTCGCAGCAGCCGACCGTGCCGGATCGTCTGCGTTGGTTATTGCAAACTTGTAAATATCAGAAAAATATTCGCATTCATGCt                                                                   >  2:255010/1‑100 (MQ=255)
                                cGAAGACAGTGCCATGTCGCAGCAGCCGACCGTGCCGGATCGTCTGCGTTGGTTATTGCAAACTTGTAAATATCAGAAAAATATTCGCATTCATGCTTTc                                                                <  1:676827/100‑1 (MQ=255)
                                    gACAGTGCCATGTCGCAGCAGCCGACCGTGCCGGATCGTCTGCGTTGGTTATTGCAAACTTGTAAATATCAGAAAAATATTCGCATTCATGCTTTCAACg                                                            <  2:686729/100‑1 (MQ=255)
                                      cAGTGCCATGTCGCAGCAGCCGACCGTGCCGGATCGTCTGCGTTGGTTATTGCAAACTTGTAAATATCAGAAAAATATTCGCATTCATGCTTTCAACGaa                                                          <  1:1645368/100‑1 (MQ=255)
                                      cAGTGCCATGTCGCAGCAGCCGACCGTGCCGGATCGTCTGCGTTGGTTATTGCAAACTTGTAAATATCAGAAAAATATTCGCATTCATGCTTTCAACGaa                                                          >  2:1851209/1‑100 (MQ=255)
                                       aGTGCCATGTCGCAGCAGCCGACCGTGCCGGATCGTCTGCGTTGGTTATTGCAAACTTTTAAATATCAGAAAAATATTCGCATTCATGCTTTCAACGAag                                                         <  1:1576799/100‑1 (MQ=255)
                                          gCCATGTCGCAGCAGCCGACCGTGCCGGATCGTCTGCGTTGGTTATTGCAAACTTGTAAATATCAGAAAAATATTCGCATTCATGCTTTCAACGAAGAgg                                                      <  1:120363/100‑1 (MQ=255)
                                           ccATGTCGCAGCAGCCGACCGTGCCGGATCGTCTGCGTTGGTTATTGCAAACTTGTAAATGTCAGAAAAATATTCGCATTCATGCTTTCAACGAAGAggg                                                     >  1:1886858/1‑100 (MQ=255)
                                           ccATGTCGCAGCAGCCGACCGTGCCGGATCGTCTGCGTTGGTTATTGCAAACTTGTAAATATCAGAAAAATATTCGCATTCATGCTTTCAACGAAGAggg                                                     >  2:986811/1‑100 (MQ=255)
                                            cATGTCGCAGCAGCCGACCGTGCCGGATCGTCTGCGTTGGTTATTGCAAACTTGTAAATATCAGAAAAATATTCGCATTCATGCTTTCAACGAAGAGGGc                                                    >  1:1989997/1‑100 (MQ=255)
                                             aTGTCGCAGCAGCCGACCGTGCCGGATCGTCTGCGTTGGTTATTGCAAACTGGTAAATGTCAGGAAAATATTCGCATTCATGCTTTCAACGAAGATGGCa                                                   >  1:1116610/1‑100 (MQ=255)
                                              tGTCGCAGCAGCCGACCGTGCCGGATCGTCTGCGTTGGTTATTGCAAACTTGTAAATATCAGAAAAATATTCGCATTCATGCTTTCAACGAAGAGGGCAt                                                  <  2:328552/100‑1 (MQ=255)
                                                tCGCAGCAGCCGACCGTGCCGGATCGTCTGCGTTGGTTATTGCAAACTTGTAAATATCAGAAAAATATTCGCATTCATGCTTTCAACGAAGAGGGCATgg                                                <  2:695954/100‑1 (MQ=255)
                                                tCGCAGCAGCCGACCGTGCCGGATCGTCTGCGTTGGTTATTGCAAACTTGTAAATATCAGAAAAATATTCGCATTCATGCTTTCAACGAAGAGGGCATgg                                                <  2:615623/100‑1 (MQ=255)
                                                 caacgcagcCGACTGTGCCGAATCGTCTGAGTTGTTTATTTTAAACTTGTAAATATCAGAAAAATATTCGCATTCATGCTTTCAACGAAGAGGGCATg                                                 <  2:307711/94‑1 (MQ=255)
                                                  gcagcaGCCGACCGTGCCGGATCGTCTGCGTTGGTTATTGCAAACTTGTAAATATCAGAAAAATATTCGCATTCATGCTTTCAACGAAGAGGGCATGGAg                                              <  1:1172829/100‑1 (MQ=255)
                                                  gcagcaGCCGACCGTGCCGGATCGTCTGCGTTGGTTATTGCAAACTTGTAAATATCAGAAAAATATTCGCATTCATGCTTTCAACGAAGAGGGCATGGAg                                              >  2:1172823/1‑100 (MQ=255)
                                                  gcagcaGCCGACCGTGCCGGATCGTCTGCGTTGGTTATTGCAAACTTGTAAATATCAGAAAAATATTCGCATTCATGCTTTCAACGAAGAGGGCATGGAg                                              >  2:1775700/1‑100 (MQ=255)
                                                   cagcagCCGACCGTGCCGGATCGTCTGCGTTGGTTATTGCAAACTTGTAAATATCAGAAAAATATTCGCATTCATGCTTTCAACGAAGAGGGCATGGAGc                                             <  2:226754/100‑1 (MQ=255)
                                                     gcagcCGACCGTGCCGGATCGTCTGCGTTGGTTATTGCAAACTTGTAAATATCAGAAAAATATTCGCATTCATGCTTTCAACGAAGAGGGCATGGAGCCg                                           <  2:1304385/100‑1 (MQ=255)
                                                     gcagcCGACCGTGCCGGATCGTCTGCGTTGGTTATTGCAAACTTGTAAATATCAGAAAAATATTCGCATTCATGCTTTCAACGAAGAGGGCATGGAGCCg                                           <  1:1972124/100‑1 (MQ=255)
                                                     gcagcCGACCGTGCCGGATCGTCTGCGTTGGTTATTGCAAACTTGTAAATATCAGAAAAATATTCGCATTCATGCTTTCAACGAAGAGGGCATGGAGCCg                                           <  2:278491/100‑1 (MQ=255)
                                                       agcCGACCGTGCCGGATCGTCTGCGTTGGTTATTGCAAACTTGTAAATATCAGAAAAATATTCGCATTCATGCTTTCAACGAAGAGGGCATGGAGCCGTa                                         >  2:184860/1‑100 (MQ=255)
                                                        gcCGACCGTGCCGGATCGTCTGCGTTGGTTATTGCAAACTTGTAAATATCAGAAAAATATTCGCATTCATGCTTTCAACGAAGCGGGCCTGGAGCCGt                                          >  1:1111896/1‑98 (MQ=255)
                                                        gcCGACCGTGCCGGATCGTCTGCGTTGGTTATTGCAAACTTGTAAATATCAGAAAAATATTCGCATTCATGCTTTCAACGAAGAGGGCATGGAGCCGTAt                                        >  2:79977/1‑100 (MQ=255)
                                                           gACCGTGCCGGATCGTCTGCGTTGGTTATTGCAAACTTGTAAATATCAGAAAAATATTCGCATTCATGCTTTCAACGAAGAGGGCATGGAGCCGTATCCg                                     <  2:1290473/100‑1 (MQ=255)
                                                           gACCGTGCCGGATCGTCTGCGTTGGTTATTGCAAACTTGTAAATATCAGAAAAATATTCGCATTCATGCTTTCAACGAAGAGGGCATGGAGCCGTATCCg                                     >  1:34017/1‑100 (MQ=255)
                                                             ccGTGCCGGATCGTCTGCGTTGGTTATTGCAAACTTGTAAATATCAGAAAAATATTCGCATTCATGCTTTCAACGAAGAGGGCATGGAGCCGTATCCGCa                                   >  1:1311057/1‑100 (MQ=255)
                                                                 gCCGGATCGTCTGCGTTGGTTATTGCAAACTTGTAAATATCAGAAAAATATTCGCATTCATGCTTTCAACGAAGAGGGCATGGAGCCGTATCCGCACGGc                               >  2:589606/1‑100 (MQ=255)
                                                                  ccGGATCGTCTGCGTTGGTTATTGCAAACTTGTAAATATCAGAAAAATATTCGCATTCATGCTTTCAACGAAGAGGGCATGGAGCCGTATCCGCACGGCt                              >  2:1878981/1‑100 (MQ=255)
                                                                   cGGATCGTCTGCGTTGGTTATTGCAAACTTGTAAATATCAGAAAAATATTCGCATTCATGCTTTCAACGAAGAGGGCATGGAGCCGTATCCGCACGGCTg                             >  2:725441/1‑100 (MQ=255)
                                                                    ggATCGTCTGCGTTGGTTATTGCAAACTTGTAAATATCAGAAAAATATTCGCATTCATGCTTTCAACGAAGAGGGCATGGAGCCGTATCCGCACGGCTgg                            <  2:1111891/100‑1 (MQ=255)
                                                                     gATCGTCTGCGTTGGTTATTGCAAACTTGTAAATATCAGAAAAATATTCGCATTCATGCTTTCAACGAAGAGGGCATGGAGCCGTATCCGCACGGCTggn                           <  1:1876884/100‑2 (MQ=255)
                                                                      aTCGTCTGCGTTGGTTATTGCAAACTTGTAAATATCAGAAAAATATTCGCATTCATGCTTTCAACGAAGAGGGCATGGAGCCGTATCCGCACGGCTGGGa                          >  2:2028302/1‑100 (MQ=255)
                                                                          tCTGCGTTGGTTATTGCAAACTTGTAAATATCAGAAAAATATTCGCATTCATGCTTTCAACGAAGAGGGCATGGAGCCGTATCCGCACGGCTGGGAtgtg                      <  1:1265906/100‑1 (MQ=255)
                                                                            tGCGTTGGTTATTGCAAACTTGTAAATATCAGAAAAATATTCGCATTCATGCTTTCAACGAAGAGGGCATGGAGCCGTATCCGCACGGCTGGGAtgtgtg                    <  1:1142077/100‑1 (MQ=255)
                                                                              cGTTGGTTATTGCAAACTTGTAAATATCAGAAAAATATTCGCATTCATGCTTTCAACGAAGAGGGCATGGAGCCGTATCCGCACGGCTGGGATGTGTGGa                  >  2:1143512/1‑100 (MQ=255)
                                                                              cGTTGGTTATTGCAAACTTGTAAATATCAGAAAAATATTCGCATTCATGCTTTCAACGAAGAGGGCATGGAGCCGTATCCGCACGGCTGGGATGTGTGGa                  >  2:103591/1‑100 (MQ=255)
                                                                               gTTGGTTATTGCAAACTTGTAAATATCAGAAAAATATTCGCATTCATGCTTTCAACGAAGAGGGCATGGAGCCGTATCCGCACGGCTGGGATGTGTGGAg                 <  2:421453/100‑1 (MQ=255)
                                                                                     tATTGCAAACTTGTAAATATCAGAAAAATATTCGCATTCATGCTTTCAACGAAGAGGGCATGGAGCCGTATCCGCACGGCTGGGATGTGTGGAGCAACgg           >  1:1639133/1‑100 (MQ=255)
                                                                                     tATTGCAAACTTGTAAATATCAGAAAAATATTCGCATTCATGCTTTCAACGAAGAGGGCATGGAGCCGTATCCGCACGGCTGGGATGTGTGGAGCAACgg           <  2:897028/100‑1 (MQ=255)
                                                                                       ttGCAAACTTGTAAATATCAGAAAAATATTCGCATTCACGCTTTCAACGAAGAGGGCATGGAGCCGTATCCGCACGGCTGGGATGTGTGGAGCAACGGCa         <  2:1116605/100‑1 (MQ=255)
                                                                                        tGCAAACTTGTAAATATCAGAAAAATATTCGCATTCATGCTTTCAACGAAGAGGGCATGGAGCCGTATCCGCACGGCTGGGATGTGTGGAGCAACGGCAt        <  1:307712/100‑1 (MQ=255)
                                                                                        tGCAAACTTGTAAATATCAGAAAAATATTCGCATTCATGCTTTCAACGAAGAGGGCATGGAGCCGTATCCGCACGGCTGGGATGTGTGGAGCAACGGCAt        >  1:125971/1‑100 (MQ=255)
                                                                                         gCAAACTTTTAAATATCAGAAAAATATTCGCATTCATGCTTTCAACGAAGAGGGCATGGAGCCGTATCCGCACGGCTGGGATGTGTGGAGCAACGGCATc       >  1:1770642/1‑100 (MQ=255)
                                                                                          cAAACTTGTAAATATCAGAACAATATTCGCATTCATGCTTTCAACGAAGAGGGCATGGAGCCGTATCCGCACGGCTGGGATGTGTGGAGCAACGGCATCa      >  2:1246224/1‑100 (MQ=255)
                                                                                          cAAACTTGTAAATATCAGAAAAATATTCGCATTCATGCTTTCAACGAAGAGGGCATGGAGCCGTATCCGCACGGCTGGGATGTGTGGAGCAACGGCATCa      <  1:1588025/100‑1 (MQ=255)
                                                                                             aCTTGTAAATATCAGAAAAATATTCGCATTCATGCTTTCAACGAAGAGGGCATGGAGCCGTATCCGCACGGCTGGGATGTGTGGAGCAACGGCATCaaaa   <  2:195852/100‑1 (MQ=255)
                                                                                              cTTGTAAATATCAGAAAAATATTCGCATTCATGCTTTCAACGAAGAGGGCATGGAGCCGTATCCGCACGGCTGGGATGTGTGGAGCAACGGCATCaaaaa  >  2:1002903/1‑100 (MQ=255)
                                                                                                 |                                                                                                
GGTTTTGACGATACCCGTGACCGCGCGTTGTTCGAAGACAGTGCCATGTCGCAGCAGCCGACCGTGCCGGATCGTCTGCGTTGGTTATTGCAAACTTTTAAATATCAGAAAAATATTCGCATTCATGCTTTCAACGAAGAGGGCATGGAGCCGTATCCGCACGGCTGGGATGTGTGGAGCAACGGCATCAAAAA  >  NC_000913/4627609‑4627802

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A