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
A138 F1 I1 R1 17 163.5 10262604 95.7% 9821312 76.0

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA REL606 3,488,791 A→C F139C (TTC→TGC)  glpR ← DNA‑binding transcriptional repressor

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*REL6063,488,7910AC99.1% 483.5 / ‑4.5 115F139C (TTC→TGC) glpRDNA‑binding transcriptional repressor
Reads supporting (aligned to +/- strand):  ref base A (1/0);  new base C (51/63);  total (52/63)
Fisher's exact test for biased strand distribution p-value = 4.52e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.80e-01

Only 100 of 121 total aligned reads displayed.

AACTGGGAGATAAAATCGAGCGTCGCTTCGCCAATGATCCCGCCATCGCGGCTGCGTAATTCGCCACCGGCGAAAATGATGCGGAAATCTTGTTTTACCATCAACGTGTTAGCAACATTGAGATTGTTGGTGACAATACGCAAATTG  >  REL606/3488719‑3488865
                                                                        |                                                                          
aaCTGGGAGATAAAATCGAGCGTCGCTTCGCCAATGATCCCGCCATCGCGGCTGCGTAATTCGCCACCGGCGcaaa                                                                         <  2:4269070/76‑1 (MQ=255)
  cTGGGAGATAAAATCGAGCGTCGCTTCGCCAATGATCCCGCCATCGCGGCTGCGTAATTCGCCACCGGCGCAAatg                                                                       >  2:3150108/1‑76 (MQ=255)
   tGGGAGATAAAATCGAGCGTCGCTTCGCCAATGATCCCGCCATCGCGGCTGCGTAATTCGCCACCGGCGCAAatga                                                                      >  1:3351193/1‑76 (MQ=255)
   tGGGAGATAAAATCGAGCGTCGCTTCGCCAATGATCCCGCCATCGCGGCTGCGTAATTCGCCACCGGCGCAAatga                                                                      >  2:4415212/1‑76 (MQ=255)
   tGGGAGATAAAATCGAGCGTCGCTTCGCCAATGATCCCGCCATCGCGGCTGCGTAATTCGCCACCGGCGCAAatga                                                                      >  1:2453508/1‑76 (MQ=255)
   tGGGAGATAAAATCGAGCGTCGCTTCGCCAATGATCCCGCCATCGCGGCTGCGTAATTCGCCACCGGCGCAAatga                                                                      >  1:4524273/1‑76 (MQ=255)
   tGGGAGATAAAATCGAGCGTCGCTTCGCCAATGATCCCGCCATCGCGGCTGCGGAAATCGCCACCGGCGAAAatga                                                                      >  1:675094/1‑76 (MQ=255)
    gggAGATAAAATCGAGCGTCGCTTCGCCAATGATCCCGCCATCGCGGCTGCGTAATTCGCCACCGGCGCAAatgat                                                                     <  2:2513633/76‑1 (MQ=255)
    gggAGATAAAATCGAGCGTCGCTTCGCCAATGATCCCGCCATCGCGGCTGCGTAATTCGCCACCGGCGCAAatgat                                                                     >  2:4456354/1‑76 (MQ=255)
    gggAGATAAAATCGAGCGTCGCTTCGCCAATGATCCCGCCATCGCGGCTGCGTAATTCGCCACCGGCGCAAatgat                                                                     <  1:3854911/76‑1 (MQ=255)
     ggAGAAAAAATCGAGCGCCGCTTCGCCAATGATCCCGCCATCGCGGCTGCGTAATTCGCCACCGGCGCAAatgatg                                                                    <  2:389444/76‑1 (MQ=255)
       agaTAAAATCGAGCGTCGCTTCGCCAATGATCCCGCCATCGCGGCTGCGTAATTCGCCACCGGCGCAAATGATGCg                                                                  <  1:2140850/76‑1 (MQ=255)
         aTAAAATCGAGCGTCGCTTCGCCAATGATCCCGCCATCGCGGCTGCGTAATTCGCCACCGGCGCAAATGATGCGGa                                                                >  1:36665/1‑76 (MQ=255)
          tAAAATCGAGGGTCGCTTCGCCAATAATCCCGCCATCGCGGCTGCGTAATTCGCCACCGGCGCAAATGATGCGGaa                                                               <  1:113671/76‑1 (MQ=255)
          tAAAATCGAGCGTCGCTTCGCCAATGATCCCGCCATCGCGGCTGCGTAATTCGCCACCGGCGCAAATGATGCGGaa                                                               >  1:2211882/1‑76 (MQ=255)
           aaaaTGGAGCGTCGCTTCGCCAATGATCCCGCCATCGCGGCTGCGTAATTCGCCACCGGCGCAAATGATGCGGaaa                                                              <  1:1660611/76‑1 (MQ=255)
           aaaaTCGAGCGTCGCTTCGCCAATGATCCCGCCATCGCGGCTGCGTAATTCGCCACCGGCGCAAATGATGCGGaaa                                                              <  1:403588/76‑1 (MQ=255)
            aaaTCGAGCGTCGCTTCGCCAATGATCCCGCCATCGCGGCTGCGTAATTCGCCACCGGCGCAAATGATGCGGAAAt                                                             <  1:4368623/76‑1 (MQ=255)
            aaaTCGAGCGTCGCTTCGCCAATGATCCCGCCATCGCGGCTGCGTAATTCGCCACCGGCGCAAATGATGCGGAAAt                                                             <  1:2713194/76‑1 (MQ=255)
            aaaTCGAGCGTCGCTTCGCCAATGATCCCGCCATCGCGGCTGCGTAATTCGCCACCGGCGCAAATGATGCGGAAAt                                                             <  2:1483274/76‑1 (MQ=255)
             aaTCGAGCGTCGCTTCGCCAATGATCCCGCCATCGCGGCTGCGTAATTCGCCACCGGCGCAAATGATGCGGAAATc                                                            >  1:2995562/1‑76 (MQ=255)
               tCGAGCGTCGCTTCGCCAATGATCCCGCCATCGCGGCTGCGTAATTCGCCACCGGCGCAAATGATGCGGAAATCtt                                                          >  1:1335495/1‑76 (MQ=255)
               tCGAGCGTCGCTTCGCCAATGATCCCGCCATCGCGGCTGCGTAATTCGCCACCGGCGCAAATGATGCGGAAATCtt                                                          <  1:4933023/76‑1 (MQ=255)
               tCGAGCGTCGCTTCGCCAATGATCCCGCCATCGCGGCTGCGTAATTCGCCACCGGCGCAAATGATGCGGAAATCtt                                                          >  1:1749532/1‑76 (MQ=255)
                cGAGCGTCGCTTCGCCAATGATCCCGCCATCGCGGCTGCGTAATTCGCCACCGGCGCAAATGATGCGGAAATCTTg                                                         >  2:3416478/1‑76 (MQ=255)
                cGAGCGTCGCTTCGCCAATGATCCCGCCATCGCGGCTGCGTAATTCGCCACCGGCGCAAATGATGCGGAAATCTTg                                                         >  2:4494095/1‑76 (MQ=255)
                 gAGCGTCGCTTCGCCAATGATCCCGCCATCGCGGCTGCGTAATTCGCCACCGGCGCAAATGATGCGGAAATCTTGt                                                        >  1:2733358/1‑76 (MQ=255)
                   gCGTCGCTTCGCCAATGATCCCGCCATCGCGGCTGCGTAATTCGCCACCGGCGCAAATGATGCGGAAATCTTGttt                                                      <  2:159370/76‑1 (MQ=255)
                    cGTCGCTTCGCCAATGATCCCGCCATCGCGGCTGCGTAATTCGCCACCGGCGCAAATGATGCGGAAATCTTGtttt                                                     >  1:3183326/1‑76 (MQ=255)
                    cGTCGCTTCGCCAATGATCCCGCCATCGCGGCTGCGTAATTCGCCACCGGCGCAAATGATGCGGAAATCTTGtttt                                                     <  2:2340276/76‑1 (MQ=255)
                     gTCCCTTCGCCAATGCCCCCGCCATCGCGGCTGCGTAATTCGCCACCGGCGCAAATGATGCGGAAATCTTGTTTTa                                                    <  1:3083313/76‑1 (MQ=255)
                       cGCTTCGCCAATGATCCCGCCATCGCGGCTGCGTAATTCGCCACCGGCGCAAATGATGCGGAAATCTTGTTTTAcc                                                  <  1:4058040/76‑1 (MQ=255)
                        gCTTCGCCAATGATCCCGCCATCGCGGCTGCGTAATTCGCCACCGGCGCAAATGTTTCGGAAATCTTGTCTTACCa                                                 >  1:3862607/1‑76 (MQ=255)
                        gCTTCGCCAATGATCCCGCCATCGCGGCTGCGTAATTCGCCACCGGCGCAAATGATGCGGAAATCTTGTTTTACCa                                                 <  1:349629/76‑1 (MQ=255)
                        gCTTCGCCAATGATCCCGCCATCGCGGCTGCGTAATTCGCCACCGGCGCAAATGATGCGGAAATCTTGTTTTACCa                                                 <  1:4342274/76‑1 (MQ=255)
                         cTTCGCCAATGATCCCGCCATCGCGGCTGCGTAATTCGCCACCGGCGCAAATGATGCGGAAATCTTGTTTTACCAt                                                >  1:3555360/1‑76 (MQ=255)
                         cTTCGCCAATGATCCCGCCATCGCGGCTGCGTAATTCGCCACCGGCGCAAATGATGCGGAAATCTTGTTTTACCAt                                                >  1:4804958/1‑76 (MQ=255)
                         cTTCGCCAATGATCCCGCCATCGCGGCTGCGTAATTCGCCACCGGCGCAAATGATGCGGAAATCATGTTTTACCAt                                                >  2:5070308/1‑76 (MQ=255)
                          ttCGCCAATGATCCCGCCATCGCGGCTGCGTAATTCGCCACCGGCGCAAATGATGCGGAAATCTTGTTTTACCATc                                               <  2:4454279/76‑1 (MQ=255)
                          ttCGCCAATGATCCCGCCATCGCGGCTGCGTAATTCGCCACCGGCGCAAATGATGCGGAAATCTTGTTTTACCATc                                               >  2:2076863/1‑76 (MQ=255)
                           tCGCCAATGATCCCGCCATCGCGGCTGCGTAATTCGCCACCGGCGCCAATGATGCGGAAATCTTGTTTTACCATCa                                              >  2:4063110/1‑76 (MQ=255)
                            cGCCAATGATCCCGCCATCGCGGCTGCGTAATTCGCCACCGGCGCAAATGATGCGGAAATCTTGTTTTACCATCaa                                             <  2:4858288/76‑1 (MQ=255)
                             gCCAATGATCCCGCCATCGCGGCTGCGTAATTCGCCACCGGCGCAAATGATGCGGAAATCTTGTTTTACCATCAAc                                            >  1:1372244/1‑76 (MQ=255)
                               cAATGATCCCGCCATCGCGGCTGCGTAATTCGCCACCGGCGCAAATGATGCGGAAATCTTGTTTTACCATCAACgt                                          >  1:1975253/1‑76 (MQ=255)
                               cAATGATCCCGCCATCGCGGCTGCGTAATTCGCCACCGGCGCAAATGATGCGGAAATCTTGTTTTACCATCAACgt                                          >  2:4718215/1‑76 (MQ=255)
                               cAATGATCCCGCCATCGCGGCTGCGTAATTCGCCACCGGCGCAAATGATGCGGAAATCTTGTTTTACCATCAACgt                                          >  2:4258065/1‑76 (MQ=255)
                                aaTGATCCCGCCATCGCGGCTGCGTAATTCGCCACCGGCGCAAATGATGCGGAAATCTTGTTTTACCATCAACgtg                                         <  2:3210173/76‑1 (MQ=255)
                                  tGATCCCGCCATCGCGGCTGCGTAATTCGCCACCGGCGCAAATGATGCGGAAATCTTGTTTTACCATCAACGTGtt                                       >  2:4064671/1‑76 (MQ=255)
                                  tGATCCCGCCATCGCGGCTGCGTAATTCGCCACCGGCGCAAATGATGCGGAAATCTTGTTTTACCATCAACGTGtt                                       <  1:4046300/76‑1 (MQ=255)
                                   gATCCCGCCATCGCGGCTGCGTAATTCGCCACCGGCGCAAATGATGCGGAAATCTTGTTTTACCATCAACGTGTTa                                      >  1:3874821/1‑76 (MQ=255)
                                   gATCCCGCCATCGCGGCTGCGTAATTCGCCACCGGCGCAAATGATGCGGAAATCTTGTTTTACCATCAACGTGTTa                                      >  1:4993473/1‑76 (MQ=255)
                                    aTCCCGCCATCGCGGCTGCGTAATTCGCCACCGGCGCAAATGATGCGGAAATCTTGTTTTACCATCAACGTGTTAg                                     >  2:964530/1‑76 (MQ=255)
                                     tCCCGCCATCGCGGCTGCGTAATTCGCCACCGGCGCAAATGATGCGGAAATCTTGTTTTACCATCAACGTGTTAGc                                    >  2:1938154/1‑76 (MQ=255)
                                       ccGCCATCGCGGCTGCGTAATTCGCCACCGGCGCAAATGATGCGGAAATCTTGTTTTACCATCAACGTGTTAGCaa                                  <  1:4171720/76‑1 (MQ=255)
                                        cGCCATCGCGGCTGCGTAATTCGCCACCGGCGCAAATGATGCGGAAATCTTGTTTTACCATCAACGTGTTAGCAAc                                 <  2:941915/76‑1 (MQ=255)
                                         gCCATCGCGGCTGCGTAATTCGCCACCGGCGCAAATGATGCGGAAATCTTGTTTTACCATCAACGTGTTAGCAACa                                <  1:1492088/76‑1 (MQ=255)
                                         gCCATCGCGGCTGCGTAATTCGCCACCGGCGCAAATGATGCGGAAATCTTGTTTTACCATCAACGTGTTAGCAACa                                <  2:4504293/76‑1 (MQ=255)
                                         gCCATCGCGGCTGCGTAATTCGCCACCGGCGCAAATGATGCGGAAATCTTGTTTTACCATCAACGTGTTAGCAACa                                <  2:1982525/76‑1 (MQ=255)
                                         gCCATCGCGGCTGCGTAATTCGCCACCGGCGCAAATGATGCGGAAATCTTGTTTTACCATCAACGTGTTAGCAACa                                <  2:4804871/76‑1 (MQ=255)
                                          ccATCGCGGCTGCGTAATTCGCCACCGGCGCAAATGATGCGGAAATCTTGTTTTACCATCAACGTGTTAGCAACAt                               <  1:4811745/76‑1 (MQ=255)
                                           cATCGCGGCTGCGTAATTCGCCACCGGCGCAAATGATGCGGAAATCTTGTTTTACCATCAACGTGTTAGCAACAtt                              >  2:4277832/1‑76 (MQ=255)
                                            aTCGCGGCTGCGTAATTCGCCACCGGCGCAAATGATGCGGAAATCTTGTTTTACCATCAACGTGTTAGCAACATTg                             <  2:698115/76‑1 (MQ=255)
                                            aTCGCGGCTGCGTAATTCGCCACCGGCGCAAATGATGCGGAAATCTTGTTTTACCATCAACGTGTTAGCAACATTg                             <  2:4446342/76‑1 (MQ=255)
                                            aTCGCGGCTGCGTAATTCGCCACCGGCGCAAATGATGCGGAAATCTTGTTTTACCATCAACGTGTTAGCAACATTg                             <  2:3206461/76‑1 (MQ=255)
                                            aTCGCGGCTGCGTAATTCGCCACCGGCGCAAATGATGCGGAAATCTTGTTTTACCATCAACGTGTTAGCAACATTg                             >  2:3291615/1‑76 (MQ=255)
                                            aTCGCGGCTGCGTAATTCGCCACCGGCGCAAATGATGCGGAAATCTTGTTTTACCATCAACGTGTTAGCAACATTg                             >  1:4048156/1‑76 (MQ=255)
                                             tCGCGGCTGCGTAATTCGCCACCGGCGCAAATGATGCGGAAATCTTGTTTTACCATCAACGTGTTAGCAACATTga                            >  2:1067626/1‑76 (MQ=255)
                                              cgcgGCTGCGTAATTCGCCACCGGCGCAAATGATGCGGAAATCTTGTTTTACCATCAACGTGTTAGCAACATTgag                           <  2:3094567/76‑1 (MQ=255)
                                               gcgGCTGCGTAATTCGCCACCGGCGCAAATGATGCGGAAATCTTGTTTTACCATCAACGTGTTAGCAACATTgaga                          >  1:1762417/1‑76 (MQ=255)
                                                 ggCTGCGTAATTCGCCACCGGCGCAAATGATGCGGAAATCTTGTTTTACCATCAACGTGTTAGCAACATTGAGAtt                        <  1:2382792/76‑1 (MQ=255)
                                                 ggCTGCGTAATTCGCCACCGGCGCAAATGATGCGGAAATCTTGTTTTACCATCAACGTGTTAGCAACATTGAGAtt                        <  1:3372982/76‑1 (MQ=255)
                                                  gCTGCGTAATTCGCCACCGGCGCAAATGATGCGGAAATCTTGTTTTACCATCAACGTGTTAGCAACATTGAGAttg                       >  2:3436907/1‑76 (MQ=255)
                                                   cTGCGTAATTCGCCACCGGCGCAAATGATGCGGAAATCTTGTTTTACCATCAACGTGTTAGCAACATTGAGAttgt                      >  1:3849063/1‑76 (MQ=255)
                                                   cTGCGTAATTCGCCACCGGCGCAAATGATGCGGAAATCTTGTTTTACCATCAACGTGTTAGCAACATTGAGAttgt                      <  1:3186936/76‑1 (MQ=255)
                                                    tGCGTAATTCGCCACCGGCGCAAATGATGCGGAAATCTTGTTTTACCATCAACGTGTTAGCAACATTGAGAttgtc                     <  1:4776151/76‑2 (MQ=255)
                                                      cGTAATTCGCCACCGGCGCAAATGATGCGGAAATCTTGTTTTACCATCAACGTGTTAGCAACATTGAGATTGTTgg                   <  1:980230/76‑1 (MQ=255)
                                                        tAATTCGCCACCGGCGCAAATGATGCGGAAATCTTGTTTTACCATCAACGTGTTAGCAACATTGAGATTGTTGGTg                 <  1:2721204/76‑1 (MQ=255)
                                                        tAATTCGCCACCGGCGCAAATGATGCGGAAATCTTGTTTTACCATCAACGTGTTAGCAACATTGAGATTGTTGGTg                 <  1:2484690/76‑1 (MQ=255)
                                                         aaTTCGCCACCGGCGCAAATGATGCGGAAATCTTGTTTTACCATCAACGTGTTAGCAACATTGAGATTGTTGGTGa                >  2:1857201/1‑76 (MQ=255)
                                                         aaTTCGCCACCGGCGCAAATGATGCGGAAATCTTGTTTTACCATCAACGTGTTAGCAACATTGAGATTGTTGGTGa                <  1:2220776/76‑1 (MQ=255)
                                                         aaTTCGCCACCGGCGCAAATGATGCGGAAATCTTGTTTTACCATCAACGTGTTAGCAACATTGAGATTGTTGGTGa                >  1:5001160/1‑76 (MQ=255)
                                                           ttCGCCACCGGCGCAAATGATGCGGAAATCTTGTTTTACCATCAACGTGTTAGCAACATTGAGATTGTTGGTGACa              <  2:3745365/76‑1 (MQ=255)
                                                             cGCCACCGGCGCAAATGATGCGGAAATCTTGTTTTACCATCAACGTGTTAGCAACATTGAGATTGTTGGTGACAAt            <  2:1080094/76‑1 (MQ=255)
                                                             cGCCACCGGCGCAAATGATGCGGAAATCTTGTTTTACCATCAACGTGTTAGCAACATTGAGATTGTTGGTGACAAt            >  1:3510370/1‑76 (MQ=255)
                                                             cGCCACCGGCGCAAATGATGCGGAAATCTTGTTTTACCATCAACGTGTTAGCAACATTGAGATTGTTGGTGACAAt            <  1:2646306/76‑1 (MQ=255)
                                                              gCCACCGGCGCAAATGATGCGGAAATCTTGTTTTACCATCAACGTGTTAGCAACATTGAGATTGTTGGTGACAATa           <  2:1270479/76‑1 (MQ=255)
                                                              gCCACCGGCGCAAATGATGCGGAAATCTTGTTTTACCATCAACGTGTTAGCAACATTGAGATTGTTGGTGACAATa           <  2:1355035/76‑1 (MQ=255)
                                                              gCCACCGGCGCAAATGATGCGGAAATCTTGTTTTACCATCAACGTGTTAGCAACATTGAGATTGTTGGTGACAATa           <  2:2642432/76‑1 (MQ=255)
                                                               ccACCGGCGCAAATGATGCGGAAATCTTGTTTTACCATCAACGTGTTAGCAACATTGAGATTGTTGGTGACAATAc          <  1:2641633/76‑1 (MQ=255)
                                                               ccACCGGCGCAAATGATGCGGAAATCTTGTTTTACCATCAACGTGTTAGCAACATTGAGATTGTTGGTGACAATAc          >  2:4249909/1‑76 (MQ=255)
                                                                cACCGGCGCAAATGATGCGGAAATCTTGTTTTACCATCAACGTGTTAGCAACATTGAGATTGTTGGTGACAATACg         <  2:2292594/76‑1 (MQ=255)
                                                                cACCGGCGCAAATGATGCGGAAATCTTGTTTTACCATCAACGTGTTAGCAACATTGAGATTGTTGGTGACAATACg         <  2:3717561/76‑1 (MQ=255)
                                                                 aCCGGCGCAAATGATGCGGAAATCTTGTTTTACCATCAACGTGTTAGCAACATTGAGATTGTTGGTGACAATACGc        >  2:536403/1‑76 (MQ=255)
                                                                  ccGGCGCAAATGATGCGGAAATCTTGTTTTACCATCAACGTGTTAGCAACATTGAGATTGTTGGTGACAATACGCa       >  2:2711631/1‑76 (MQ=255)
                                                                  ccGGCGCAAATGATGCGGAAATCTTGTTTTACCATCAACGTGTTAGCAACATTGAGATTGTTGGTGACAATACGCa       <  1:1821299/76‑1 (MQ=255)
                                                                  ccGGCGCAAATGATGCGGAAATCTTGTTTTACCATCAACGTGTTAGCAACATTGAGATTGTTGGTGACAATACGCa       >  2:4114369/1‑76 (MQ=255)
                                                                  ccGGCGCAAATGATGCGGAAATCTTGTTTTACCATCAACGTGTTAGCAACATTGAGATTGTTGGTGACAATACGCa       <  1:4149124/76‑1 (MQ=255)
                                                                    ggCGCAAATGATGCGGAAATCTTGTTTTACCATCAACGTGTTAGCAACATTGAGATTGTTGGTGACAATACGCaaa     <  2:1632509/76‑1 (MQ=255)
                                                                     gcgcAAATGATGCGGAAATCTTGTTTTACCATCAACGTGTTAGCAACATTGAGATTGTTGGTGACAATACGCAAAt    <  2:777355/76‑1 (MQ=255)
                                                                       gAAAATGATGCGGAAATCTTGTTTTACCATCAACGTGTTAGCAACATTGAGATTGTTGGTGACAATACGCAAATTg  >  2:4192993/1‑76 (MQ=255)
                                                                        |                                                                          
AACTGGGAGATAAAATCGAGCGTCGCTTCGCCAATGATCCCGCCATCGCGGCTGCGTAATTCGCCACCGGCGAAAATGATGCGGAAATCTTGTTTTACCATCAACGTGTTAGCAACATTGAGATTGTTGGTGACAATACGCAAATTG  >  REL606/3488719‑3488865

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A