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 2,130,622 T→C 12.6% I95V (ATT→GTT)  mtr ← tryptophan transporter of high affinity

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,130,6220TC12.6% 268.6 / 25.0 103I95V (ATT→GTT) mtrtryptophan transporter of high affinity
Reads supporting (aligned to +/- strand):  ref base T (32/58);  new base C (9/4);  total (41/62)
Fisher's exact test for biased strand distribution p-value = 3.19e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

Only 100 of 107 total aligned reads displayed.

GGTGTGATGCAGAATCGAACCACTGGCAGAAATATAGGCATAGGTCAGGATATAGAGCACAAAGGCAATGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCAAATCTTTGGTGATGGTGTCAAAACTCGAACC  >  minE/2130554‑2130691
                                                                    |                                                                     
ggTGTGATGCAGAATCGAACCACTGGCAGAAATATAGGCATAGGTCAGGATATAGAGCACAAAGGCAATg                                                                      >  1:2699596/1‑70 (MQ=255)
 gtgtGATGCAGAATCGAACCACTGGCAGAAATATAGGCATAGGTCAGGATATAGAGCACAAAGGCAATgg                                                                     >  1:1830348/1‑70 (MQ=255)
    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)
             aTCGAACCACTGGCAGAAATATAGGCATAGGTCAGGATATAGAGCACAAAGGCAATGGAAATGCCGt                                                            <  1:2570390/67‑1 (MQ=255)
             aTCGAACCACTGGCAGAAATATAGGCATAGGTCAGGATATAGAGCACAAAGGCAATGGAAATGCCGt                                                            <  1:220924/67‑1 (MQ=255)
              tCGAACCACTGGCAGAAATATAGGCATAGGTCAGGATATAGAGCACAAAGGCAAt                                                                       >  1:615111/1‑55 (MQ=255)
              tCGAACCACTGGCAGAAATATAGGCATAGGTCAGGATATAGAGCACAAAGGCAATGGAAATGCCGTTGAc                                                        >  1:2752857/1‑70 (MQ=255)
              tCGAACCACTGGCAGAAATATAGGCATAGGTCAGGATATAGAGCACAAAGGCAATGGAAATGCCGTTGAc                                                        >  1:1333389/1‑70 (MQ=255)
               cGAACCACTGGCAGAAATATAGGCATAGGTCAGGATATAGAGCACAAAGGCAATGGaa                                                                   <  1:2238363/58‑1 (MQ=255)
                gAACCACTGGCAGAAATATAGGCATAGGTCAGGATATAGAGCACAAAGGCAATGGAAATGCCGTTGACCAc                                                     >  1:431476/1‑71 (MQ=255)
                gAACCACTGGCAGAAATATAGGCATAGGTCAGGATATAGAGCACAAAGGCAATGGAAATGCCGTTGACCAc                                                     >  1:3038275/1‑71 (MQ=255)
                 caCCATTAGCAGAGATATAGGCATAAGTGAGGATATAGAGAACGAAGGCAACGGTAAta                                                                >  1:578192/2‑58 (MQ=255)
                 caCCATTAGCAGAGATATAGGCATAAGTGAGGATATAGAGAACGAAGGCAACGGTAAta                                                                >  1:2801671/2‑58 (MQ=255)
                  aCCATTAGCAGAGATATAGGCATAAGTGAGGATATAGAGAACGAAGGCAACGGTAAtac                                                               >  1:2706079/1‑57 (MQ=255)
                  aCCACTGGCAGAAATATAGGCATAGGTCAGGATATAGAGCACAAAGGCAATGGAAATGCCGTTGACCACGt                                                   <  1:2963379/71‑1 (MQ=255)
                  aCCACTGGCAGAAATATAGGCATAGGTCAGGATATAGAGCACAAAGGCAATGGAAATGCCGTTGACCACGt                                                   <  1:1730270/71‑1 (MQ=255)
                   ccACTGGCAGAAATATAGGCATAGGTCAGGATATAGAGCACAAAGGCAATg                                                                      >  1:3844157/1‑51 (MQ=255)
                   ccACTGGCAGAAATATAGGCATAGGTCAGGATATAGAGCACAAAGGCAATGGAAATGc                                                               >  1:1487521/1‑58 (MQ=255)
                    cACTGGCAGAAATATAGGCATAGGTCAGGATATAGAGCACAAAGGCAATGGAAATGCCGtt                                                           <  1:2286262/61‑1 (MQ=255)
                    cACTGGCAGAAATATAGGCATAGGTCAGGATATAGAGCACAAAGGCAATGGAAATGCCGtt                                                           <  1:645678/61‑1 (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)
                                 ataGGCATAGGTCAGGATATAGAGCACAAAGGCAATgg                                                                     <  1:1976668/38‑1 (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                          <  1:2512851/71‑1 (MQ=255)
                                           gTCAGGATATAGAGCACAAAGGCAATGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCAAATCttt                          <  1:2810825/71‑1 (MQ=255)
                                            tCAGGATATAGAGCACAAAGGCAATGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCAAATCTTTg                         <  1:2372374/71‑1 (MQ=255)
                                              aGGATATAGAGCACAAAGGCAATGGAAATGCCGTTGACCACGTTCCAGc                                             <  1:2374901/49‑1 (MQ=255)
                                              aGGATATAGAGCACAAAGGCAATGGAAATGCCGTTGACCACGTTCCAGc                                             <  1:596894/49‑1 (MQ=255)
                                              aGGATATAGAGCACAAAGGCAATGGAAATGCCGTTGACCACGTTCCAGc                                             <  1:2156590/49‑1 (MQ=255)
                                               gtatatatAGCACAAAGGCAATGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCaaa                               <  1:769920/60‑1 (MQ=255)
                                                gATATAGAGCACAAAGGCAATGGAAATGCCGTTGACCACGTTCCAGc                                             <  1:1485245/47‑1 (MQ=255)
                                                 atatAGAGCACAAAGGCAATGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCAAATCTTTGGTGAt                    >  1:3774950/1‑71 (MQ=255)
                                                 atatAGAGCACAAAGGCAATGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCAAATCTTTGGTGAt                    <  1:3234720/71‑1 (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                 >  1:1037977/1‑71 (MQ=255)
                                                    taGAGCACAAAGGCAATGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCAAATCTTTGGTGATGgt                 >  1:1700784/1‑71 (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            <  1:3182582/71‑1 (MQ=255)
                                                         cacaAAGGCAATGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCAAATCTTTGGTGATGGTGTCaa            <  1:507759/71‑1 (MQ=255)
                                                         cacaAAGGCAATGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCAAATCTTTGGTGATGGTGTCaa            <  1:1773326/71‑1 (MQ=255)
                                                          acgaaGGCAACGGTAATACCGCTGATAATGTTCCAGGTGTTACCGATTAAATCTTTGGTGATGGTGTTaa            >  1:620774/4‑70 (MQ=255)
                                                          acgaaGGCAACGGTAATACCGCTGATAATGTTCCAGGTGTTACCGATTAAATCTTTGGTGATGGTGTTaa            >  1:2643147/4‑70 (MQ=255)
                                                          acaAAGGCAATGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCAAATCTTTGGTGATGGTGTCaa            >  1:3648120/1‑70 (MQ=255)
                                                          acaAAGGCAATGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCAAATCTTTGGTGATGGTGTCaa            <  1:2348795/70‑1 (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)
                                                                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  <  1:1703473/71‑1 (MQ=255)
                                                                   aTGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCAAATCTTTGGTGATGGTGTCAAAACTCGAAcc  >  1:1096749/1‑71 (MQ=255)
                                                                   aTGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCAAATCTTTGGTGATGGTGTCAAAACTCGAAcc  <  1:2346839/71‑1 (MQ=255)
                                                                   aTGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCAAATCTTTGGTGATGGTGTCAAAACTCGAAcc  >  1:2725876/1‑71 (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)
                                                                    |                                                                     
GGTGTGATGCAGAATCGAACCACTGGCAGAAATATAGGCATAGGTCAGGATATAGAGCACAAAGGCAATGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCAAATCTTTGGTGATGGTGTCAAAACTCGAACC  >  minE/2130554‑2130691

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