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 F21 I0 R1 2169 63.0 3952800 76.2% 3012033 62.4

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 2,130,625 A→T 12.2% S94T (TCC→ACC)  mtr ← tryptophan transporter of high affinity

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,130,6250AT12.2% 288.0 / 26.1 106S94T (TCC→ACC) mtrtryptophan transporter of high affinity
Reads supporting (aligned to +/- strand):  ref base A (38/55);  new base T (9/4);  total (47/59)
Fisher's exact test for biased strand distribution p-value = 7.42e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

Only 100 of 107 total aligned reads displayed.

TGATGCAGAATCGAACCACTGGCAGAAATATAGGCATAGGTCAGGATATAGAGCACAAAGGCAATGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCAAATCTTTGGTGATGGTGTCAAAACTCGAACCGA  >  minE/2130558‑2130693
                                                                   |                                                                    
tgATGCAGAATCGAACCACTGGCAGAAATATAGGCATAGGTCAGGATATAGAGCACAAAGGCAATGGAAAt                                                                   >  1:816929/1‑71 (MQ=255)
  aTGCAGAATCGAACCACTGGCAGAAATATAGGCATAGGTCAGGATATAGAGCACAAAGGCAATGGAAATGc                                                                 >  1:3756300/1‑71 (MQ=255)
     cAGAATCGAACCACTGGCAGAAATATAGGCATAGGTCAGGATATAGAGCACAAAGGCAATGGAAATGCCg                                                               <  1:3419028/70‑1 (MQ=255)
     cAGAATCGAACCACTGGCAGAAATATAGGCATAGGTCAGGATATAGAGCACAAAGGCAATGGAAATGCCg                                                               <  1:313305/70‑1 (MQ=255)
     cAGAATCGAACCACTGGCAGAAATATAGGCATAGGTCAGGATATAGAGCACAAAGGCAATGGAAATGCCg                                                               <  1:2476653/70‑1 (MQ=255)
      aGAATCGAACCACTGGCAGAAATATAGGCATAGGTCAGGATATAGAGCACAAAGGCAATGGAAATGCCGtt                                                             >  1:3841630/1‑71 (MQ=255)
       gAATCGAACCACTGGCAGAAATATAGGCATAGGTCAGGATATAGAGCACAAAGGCAATGGAAATGCCGtt                                                             >  1:3882045/1‑70 (MQ=255)
       gAATCGAACCACTGGCAGAAATATAGGCATAGGTCAGGATATAGAGCACAAAGGCAATGGAAATGCCGTTg                                                            <  1:3419420/71‑1 (MQ=255)
         aTCGCACCATTAGCAGAGATATAGGCATAAGTGAGGATATAGAGAACGAAGGCAACGGTAATACCGCTGa                                                           >  1:2638131/1‑70 (MQ=255)
          tCGAACCACTGGCAGAAATATAGGCATAGGTCAGGATATAGAGCACAAAGGCAATGGAAATGCCGTTGAc                                                          >  1:1333389/1‑70 (MQ=255)
          tCGAACCACTGGCAGAAATATAGGCATAGGTCAGGATATAGAGCACAAAGGCAATGGAAATGCCGTTGAc                                                          >  1:2752857/1‑70 (MQ=255)
           cGAACCACTGGCAGAAATATAGGCATAGGTCAGGATATAGAGCACAAAGGCAATGGaa                                                                     <  1:2238363/58‑1 (MQ=255)
            gAACCACTGGCAGAAATATAGGCATAGGTCAGGATATAGAGCACAAAGGCAATGGAAATGCCGTTGACCAc                                                       >  1:3038275/1‑71 (MQ=255)
            gAACCACTGGCAGAAATATAGGCATAGGTCAGGATATAGAGCACAAAGGCAATGGAAATGCCGTTGACCAc                                                       >  1:431476/1‑71 (MQ=255)
             caCCATTAGCAGAGATATAGGCATAAGTGAGGATATAGAGAACGAAGGCAACGGTAAta                                                                  >  1:2801671/2‑58 (MQ=255)
             caCCATTAGCAGAGATATAGGCATAAGTGAGGATATAGAGAACGAAGGCAACGGTAAta                                                                  >  1:578192/2‑58 (MQ=255)
              aCCATTAGCAGAGATATAGGCATAAGTGAGGATATAGAGAACGAAGGCAACGGTAAtac                                                                 >  1:2706079/1‑57 (MQ=255)
              aCCACTGGCAGAAATATAGGCATAGGTCAGGATATAGAGCACAAAGGCAATGGAAATGCCGTTGACCACGt                                                     <  1:1730270/71‑1 (MQ=255)
              aCCACTGGCAGAAATATAGGCATAGGTCAGGATATAGAGCACAAAGGCAATGGAAATGCCGTTGACCACGt                                                     <  1:2963379/71‑1 (MQ=255)
               ccACTGGCAGAAATATAGGCATAGGTCAGGATATAGAGCACAAAGGCAATGGAAATGc                                                                 >  1:1487521/1‑58 (MQ=255)
                cACTGGCAGAAATATAGGCATAGGTCAGGATATAGAGCACAAAGGCAATGGAAATGCCGtt                                                             <  1:645678/61‑1 (MQ=255)
                cACTGGCAGAAATATAGGCATAGGTCAGGATATAGAGCACAAAGGCAATGGAAATGCCGtt                                                             <  1:2286262/61‑1 (MQ=255)
                   tGGCAGAAATATAGGCATAGGTCAGGATATAGAGCACAAAGGCAATGGAAATGCCGTTGACCACGTTCCAg                                                >  1:1530889/1‑71 (MQ=255)
                     gCAGAGATATAGGCATAAGTGAGGATATAGAGAACGAAGGCAACGGTAATACCGCTGATAATGTTCCAggt                                              <  1:2258372/71‑3 (MQ=255)
                      cAGAGATATAGGCATAAGTGAGGATATAGAGAACGAAGGCAACGGTAATACCGCTGataa                                                        <  1:2207693/60‑4 (MQ=255)
                      cAGAAATATAGGCATAGGTCAGGATATAGAGCACAAAGGCAATGGAAATGCCGTTGACCACGTTCCAGCCt                                             <  1:3900250/71‑1 (MQ=255)
                      cAGAAATATAGGCATAGGTCAGGATATAGAGCACAAAGGCAATGGAAATGCCGTTGACCACGTTCCAGCCt                                             <  1:631903/71‑1 (MQ=255)
                       aGAAATATAGGCATAGGTCAGGATATAGAGCACAAAGGCAATGGAAATGCCGtt                                                             <  1:315029/54‑1 (MQ=255)
                       aGAAATATAGGCATAGGTCAGGATATAGAGCACAAAGGCAATGGAAATGCCGTTGACCACGTTc                                                   <  1:1768982/64‑1 (MQ=255)
                       aGAAATATAGGCATAGGTCAGGATATAGAGCACAAAGGCAATGGAAATGCCGTTGACCACGTTCCAGCCtt                                            <  1:3786149/71‑1 (MQ=255)
                       aGAAATATAGGCATAGGTCAGGATATAGAGCACAAAGGCAATGGAAATGCCGTTGACCACGTTCCAGCCt                                             <  1:476426/70‑1 (MQ=255)
                         aaaTATAGGCATAGGTCAGGATATAGAGCACAAAGGCAATGGAAATGCCGTTGACCACGTTCCAGCCTTTg                                          <  1:2108386/71‑1 (MQ=255)
                            tataGGCATAGGTCAGGATATAGAGCACAAAGGCAATGGAAATGCCGTTGACCACGTTCCAGCCTTTGcc                                        <  1:1300912/70‑1 (MQ=255)
                              taGGCATAGGTCAGGATATAGAGCACAAAGGCAATGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCa                                      <  1:205213/70‑1 (MQ=255)
                               aGGCATAGGTCAGGATATAGAGCACAAAGGCAATGGAAATGCCGTTg                                                            <  1:159205/47‑1 (MQ=255)
                                ggCATACGTCAGGATATAGAGCACAAAGGCAATGGAAATGCCGtt                                                             <  1:267439/45‑1 (MQ=255)
                                 gCATAGGTCAGGATATAGAGCACAAAGGCAATGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCaa                                  <  1:2968351/71‑1 (MQ=255)
                                   aTAGGTCAGGATATAGAGCACAAAGGCAATGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGc                                    <  1:3927449/67‑1 (MQ=255)
                                    tAGGTCAGGATATAGAGCACAAAGGCAATGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCAAATc                               >  1:79700/1‑71 (MQ=255)
                                     aGGTCAGGATATAGAGCACAAAGGCAATGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCAAATCt                              >  1:342043/1‑71 (MQ=255)
                                     aGGTCAGGATATAGAGCACAAAGGCAATGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCAAATCt                              >  1:680087/1‑71 (MQ=255)
                                      ggTCAGGATATAGAGCACAAAGGCAATGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCAAATCtt                             <  1:2775292/71‑1 (MQ=255)
                                      ggTCAGGATATAGAGCACAAAGGCAATGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCAAATCt                              <  1:1548219/70‑1 (MQ=255)
                                       gTCAGGATATAGAGCACAAAGGCAATGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCAAATCttt                            <  1:2810825/71‑1 (MQ=255)
                                       gTCAGGATATAGAGCACAAAGGCAATGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCAAATCttt                            <  1:2512851/71‑1 (MQ=255)
                                        tCAGGATATAGAGCACAAAGGCAATGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCAAATCTTTg                           <  1:2372374/71‑1 (MQ=255)
                                          aGGATATAGAGCACAAAGGCAATGGAAATGCCGTTGACCACGTTCCAGc                                               <  1:596894/49‑1 (MQ=255)
                                          aGGATATAGAGCACAAAGGCAATGGAAATGCCGTTGACCACGTTCCAGc                                               <  1:2374901/49‑1 (MQ=255)
                                          aGGATATAGAGCACAAAGGCAATGGAAATGCCGTTGACCACGTTCCAGc                                               <  1:2156590/49‑1 (MQ=255)
                                           gtatatatAGCACAAAGGCAATGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCaaa                                 <  1:769920/60‑1 (MQ=255)
                                            gATATAGAGCACAAAGGCAATGGAAATGCCGTTGACCACGTTCCAGc                                               <  1:1485245/47‑1 (MQ=255)
                                             atatAGAGCACAAAGGCAATGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCAAATCTTTGGTGAt                      <  1:3234720/71‑1 (MQ=255)
                                             atatAGAGCACAAAGGCAATGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCAAATCTTTGGTGAt                      >  1:3774950/1‑71 (MQ=255)
                                             atatAGAGCACAAAGGCAATGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCAAATCTTTGGTGAt                      >  1:1591118/1‑71 (MQ=255)
                                              tataGAGCACAAAGGCAATGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCaa                                  <  1:3151871/58‑1 (MQ=255)
                                               ataGAGAACGAAGGCAACGGTAATACCGCTGATAATGTTCCAGGTGTTACCGATTAAATCTTTGGTGATgg                    >  1:2353629/1‑71 (MQ=255)
                                               ataGAGAACGAAGGCAACGGTAATACCGCTGATAATGTTCCAGGTGTTACCGATTAAATCTTTGGTGATgg                    >  1:398382/1‑71 (MQ=255)
                                                taGAGCACTAAGGCAATGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCAAATCTTTGGTGATGgt                   <  1:177020/71‑1 (MQ=255)
                                                taGAGCACAAAGGCAATGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCAAATCTTTGGTGATgg                    <  1:3634079/70‑1 (MQ=255)
                                                taGAGCACAAAGGCAATGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCAAATCTTTGGTGATGgt                   <  1:2526857/71‑1 (MQ=255)
                                                taGAGCACAAAGGCAATGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCAAATCTTTGGTGATGgt                   >  1:1037977/1‑71 (MQ=255)
                                                taGAGCACAAAGGCAATGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCAAATCTTTGGTGATGgt                   >  1:1700784/1‑71 (MQ=255)
                                                taGAGAACGAAGGCAACGGTAATACCGCTGATAATGTTCCAGGTGTTACCGATTAAATCTTTGGTGATGgt                   <  1:1728274/71‑1 (MQ=255)
                                                 agagCACAAAGGCAATGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCAAATCTTTGGTGATGgt                   >  1:378976/1‑70 (MQ=255)
                                                  gagCACAAAGGCAATGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCAAATCTTTGGTGATGgtg                  <  1:2954836/70‑1 (MQ=255)
                                                    gCACAAAGGCAATGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCAAATCTTTGGTGATGGTGTc                <  1:2107454/70‑1 (MQ=255)
                                                     cacaAAGGCAATGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCAAATCTTTGGTGAt                      <  1:58497/63‑1 (MQ=255)
                                                     cacaAAGGCAATGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCAAATCTTTGGTGATGGTGTCaa              <  1:507759/71‑1 (MQ=255)
                                                     cacaAAGGCAATGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCAAATCTTTGGTGATGGTGTCaa              <  1:3182582/71‑1 (MQ=255)
                                                     cacaAAGGCAATGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCAAATCTTTGGTGATGGTGTCaa              <  1:1773326/71‑1 (MQ=255)
                                                      acgaaGGCAACGGTAATACCGCTGATAATGTTCCAGGTGTTACCGATTAAATCTTTGGTGATGGTGTTaa              >  1:2643147/4‑70 (MQ=255)
                                                      acgaaGGCAACGGTAATACCGCTGATAATGTTCCAGGTGTTACCGATTAAATCTTTGGTGATGGTGTTaa              >  1:620774/4‑70 (MQ=255)
                                                      acaAAGGCAATGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCAAATCTTTGGTGATGGTGTCaa              <  1:2348795/70‑1 (MQ=255)
                                                      acaAAGGCAATGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCAAATCTTTGGTGATGGTGTCaa              >  1:3648120/1‑70 (MQ=255)
                                                       caAAGGCAATGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCAAATCttt                            >  1:2175401/1‑55 (MQ=255)
                                                       caAAGGCAATGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCAAATCttt                            >  1:3412681/1‑55 (MQ=255)
                                                       caAAGGCAATGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCAAATCTTTGGTGATGGTGTCaaaa            <  1:1876149/71‑1 (MQ=255)
                                                         aaGGCAATGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCAAATCTTTg                           >  1:1053184/1‑54 (MQ=255)
                                                         aaGGCAATGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCAAATCTTTg                           >  1:3254630/1‑54 (MQ=255)
                                                         aaGGCAATGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCAAATCTTTGGTGATGGTGTCAAAACt          <  1:2386780/71‑1 (MQ=255)
                                                          aGGCAATGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCAAATCTTTGGTGATGGTGTCAAAACTc         >  1:3152333/1‑71 (MQ=255)
                                                          aGGCAATGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCAAATCTTTGGTGATGGTGTCAAAACTc         <  1:2069571/71‑1 (MQ=255)
                                                          aGGCAACGGTAATACCGCTGATAATGTTCCAGGTGTTACCGATTAAATCTTTGGTGATGGTGTTAAAACtg         >  1:643712/1‑70 (MQ=255)
                                                            gCAATGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCAAATCtt                             <  1:837689/49‑1 (MQ=255)
                                                            gCAATGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCAAATCTTTGGTGATGGTGTCAAAACTCGa       <  1:1154618/71‑1 (MQ=255)
                                                              aaTGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCAAATCTTTg                           >  1:1236744/1‑49 (MQ=255)
                                                               aTGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCAAATCTTTGGt                         <  1:1991982/50‑1 (MQ=255)
                                                               aTGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCAAATCTTTGGTGATGGTGTCaa              <  1:467502/61‑1 (MQ=255)
                                                               aTGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCAAATCTTTGGTGATGGTGTCAAAACTCGAAcc    >  1:2725876/1‑71 (MQ=255)
                                                               aTGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCAAATCTTTGGTGATGGTGTCAAAACTCGAAcc    <  1:2346839/71‑1 (MQ=255)
                                                               aTGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCAAATCTTTGGTGATGGTGTCAAAACTCGAAcc    >  1:1096749/1‑71 (MQ=255)
                                                               aTGGAAATGACGTTGACCACGTTCCAGCCTTTGCCCAGCAAATCTTTGGTGATGGTGTCAAAACTCGAAcc    >  1:787359/1‑71 (MQ=255)
                                                                tGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCAAATCTTTGGTGATGGTGTCAAAACt          >  1:2888344/1‑64 (MQ=255)
                                                                tGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCAAATCTTTGGTGATGGTGTCAAAACt          >  1:696586/1‑64 (MQ=255)
                                                                tGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCAAATCTTTGGTGATGGTGTCAAAACTCGAAcc    >  1:2521322/1‑70 (MQ=255)
                                                                 ggAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCAAATCTTTGGTGATGgtgt                 >  1:3820079/1‑56 (MQ=255)
                                                                 ggAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCAAATCTTTGGTGATGGTGTCAAAACTCGAACCGa  >  1:3016953/1‑71 (MQ=255)
                                                                  gAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCAAAt                                >  1:2238315/1‑40 (MQ=255)
                                                                  gAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCAAAt                                >  1:1531108/1‑40 (MQ=255)
                                                                  gAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCAAATCTTTGGTGATGGTGTCAAAACt          >  1:3011779/1‑62 (MQ=255)
                                                                   |                                                                    
TGATGCAGAATCGAACCACTGGCAGAAATATAGGCATAGGTCAGGATATAGAGCACAAAGGCAATGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCAAATCTTTGGTGATGGTGTCAAAACTCGAACCGA  >  minE/2130558‑2130693

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