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 2,130,625 A→T 21.5% 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
*minE2,130,6250AT21.5% 283.3 / 75.4 135S94T (TCC→ACC) mtrtryptophan transporter of high affinity
Reads supporting (aligned to +/- strand):  ref base A (54/52);  new base T (14/15);  total (68/67)
Fisher's exact test for biased strand distribution p-value = 8.36e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.49e-01

Only 100 of 152 total aligned reads displayed.

GTGTGATGCAGAATCGAACCACTGGCAGAAATATAGGCATAGGTCAGGATATAGAGCACAAAGGCAATGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCAAATCTTTGGTGATGGTGTCAAAACTCGAACCGATT  >  minE/2130555‑2130695
                                                                      |                                                                      
     aTGCAGAATCGAACCACTGGCAGAAATATAGGCATAGGTCAGGATATAGAGCACAAAGGCAATGGAAATGc                                                                   >  1:3914307/1‑71 (MQ=255)
         aGAATCGAACCACTGGCAGAAATATAGGCATAGGTCAGGATATAGAGCACAAAGGCAATGGAAATGCCGtt                                                               <  1:2573442/71‑1 (MQ=255)
         aGAATCGAACCACTGGCAGAAATATAGGCATAGGTCAGGATATAGAGCACAAAGGCAATGGAAATGCCGtt                                                               <  1:4577236/71‑1 (MQ=255)
          gAATCGAACCACTGGCAGAAATATAGGCATAGGTCAGGATATAGAGCACAAAGGCAATGGa                                                                        <  1:2594640/61‑1 (MQ=255)
          gAATCGAACCACTGGCAGAAATATAGGCATAGGTCAGGATATAGAGCACAAAGGCAATGGa                                                                        <  1:126007/61‑1 (MQ=255)
          gAATCGAACCACTGGCAGAAATATAGGCATAGGTCAGGATATAGAGCACAAAGGCAATGGAAATGCCGtt                                                               >  1:4628389/1‑70 (MQ=255)
            aTCGCACCATTAGCAGAGATATAGGCATAAGTGAGGATATAGAGAACGAAGGCAACGGTAATACCGCTGat                                                            <  1:4173012/71‑2 (MQ=255)
            aTCGCACCATTAGCAGAGATATAGGCATAAGTGAGGATATAGAGAACGAAGGCAACGGTAATACCGCTGat                                                            <  1:5186317/71‑2 (MQ=255)
             tCGAACCACTGGCAGAAATATAGGCATAGGTCAGGATATAGAGCACAAAGGCAATGGaa                                                                       <  1:1585121/59‑1 (MQ=255)
             tCGAACCACTGGCAGAAATATAGGCATAGGTCAGGATATAGAGCACAAAGGCAATGGAAATGCCGTTGAc                                                            >  1:2932335/1‑70 (MQ=255)
             tCGAACCACTGGCAGAAATATAGGCATAGGTCAGGATATAGAGCACAAAGGCAATGGAAATGCCGTTGAc                                                            >  1:2605545/1‑70 (MQ=255)
              cGAACCACTGGCAGAAATATAGGCATAGGTCAGGATATAGAGCACAAAGGCAATGGaaa                                                                      >  1:3640919/1‑59 (MQ=255)
              cGAACCACTGGCAGAAATATAGGCATAGGTCAGGATATAGAGCACAAAGGCAATGGaaa                                                                      >  1:3769785/1‑59 (MQ=255)
               gAACCACTGGCAGAAATATAGGCATAGGTCAGGATATAGAGCACAAAGGCAATGGAAATGCCGTTGACCa                                                          >  1:1514809/1‑70 (MQ=255)
                   cACTGGCAGAAATATAGGCATAGGTCAGGATATAGAGCACAAAGGCAATGGAAATGCCGTTGACCACGTTc                                                     <  1:4121138/71‑1 (MQ=255)
                     cTGGCAGAAATATAGGCATAGGTCAGGATATAGAGCACAAAGGCAATGGAAATGCCGTTGACCa                                                          >  1:1605069/1‑64 (MQ=255)
                     cTGGCAGAAATATAGGCATAGGTCAGGATATAGAGCACAAAGGCAATGGAAATGCCGTTGACCACGt                                                       <  1:2089049/67‑1 (MQ=255)
                     cTGGCAGAAATATAGGCATAGGTCAGGATATAGAGCACAAAGGCAATGGAAATGCCGTTGACCACGTTc                                                     >  1:2427702/1‑69 (MQ=255)
                       ggCAGAAATATAGGCATAGGTCAGGATATAGAGCACAAAGGCAATGGAAATGCCGTTGACCACGTTCCAGc                                                 >  1:4870493/1‑71 (MQ=255)
                       agCAGAGATATAGGCATAAGTGAGGATATAGAGAACGAAGGCAACGGTAATACCGCTGa                                                             <  1:1761793/58‑1 (MQ=255)
                        gCAGAGATATAGGCATAAGTGAGGATATAGAGAACGAAGGCAACGGTAATACCGCTGATAATGTTCCAgg                                                 >  1:3911616/1‑69 (MQ=255)
                          agagATATAGGCATAAGTGAGGATATAGAGAACGAAGGCAACGGtaa                                                                      >  1:2682723/1‑47 (MQ=255)
                          agagATATAGGCATAAGTGAGGATATAGAGAACGAAGGCAACGGtaa                                                                      >  1:1194759/1‑47 (MQ=255)
                          agagATATAGGCATAAGTGAGGATATAGAGAACGAAGGCAACGGtaa                                                                      >  1:3960139/1‑47 (MQ=255)
                            agatatAGGCATAAGTGAGGATATAGAGAACGAAGGCAACGGTAATACCGCTGATAATGTTcc                                                    >  1:2501159/3‑63 (MQ=255)
                            agatatAGGCATAAGTGAGGATATAGAGAACGAAGGCAACGGTAATACCGCTGATAATGTTcc                                                    >  1:2351582/3‑63 (MQ=255)
                            agatatAGGCATAAGTGAGGATATAGAGAACGAAGGCAACGGTAATACCGCTGATAATGTTcc                                                    >  1:2284749/3‑63 (MQ=255)
                            agatatAGGCATAAGTGAGGATATAGAGAACGAAGGCAACGGTAATACCGCTGATAATGTTcc                                                    >  1:4209174/3‑63 (MQ=255)
                            agatatAGGCATAAGTGAGGATATAGAGAACGAAGGCAACGGTAATACCGCTGATAATGTTcc                                                    >  1:5092420/3‑63 (MQ=255)
                            agatatAGGCATAAGTGAGGATATAAAGAACGAAGGCAACGGTAATACCGCTGATAATGTTcc                                                    >  1:5638411/3‑63 (MQ=255)
                              atatAGGCATAGGTCAGGATATAGAGCACAAAGGCAATGGAAATGCCGTTGACCACGTTCCa                                                   >  1:1084562/1‑62 (MQ=255)
                              atatAGGCATAGGTCAGGATATAGAGCACAAAGGCAATGGAAATGCCGTTGACCACGTTCCa                                                   >  1:2791634/1‑62 (MQ=255)
                              atatAGGCATAGGTCAGGATATAGAGCACAAAGGCAATGGAAATGCCGTTGACCACGTTCCAGCCTTTGcc                                          >  1:1800618/1‑71 (MQ=255)
                              atatAGGCATAGGTCAGGATATAGAGCACAAAGGCAATGGAAATGCCGTTGACCACGTTCCAGCCTTTGcc                                          <  1:3590723/71‑1 (MQ=255)
                               tataGGCATAGGTCAGGATATAGAGCACAAAGGCAATGGAAATGCCGTTGACCACGTTCCAGCCTTTGccc                                         <  1:2750719/71‑1 (MQ=255)
                                ataGGCATAGGTCAGGATATAGAGCACAAAGGCAATGGAAATGCCGTTGACCACGTTCCAGCCTTTGcc                                          <  1:5230412/69‑1 (MQ=255)
                                 taGGCATAGGTCAGGATATAGAGCACAAAGGCAATGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAg                                       >  1:17965/1‑71 (MQ=255)
                                 taGGCATAAGTGAGGATATAGAGAACGAAGGCAACGGTAATACCGCTGat                                                            <  1:652054/50‑2 (MQ=255)
                                 taGGCATAAGTGAGGATATAGAGAACGAAGGCAACGGTAATACCGCTGat                                                            <  1:1651353/50‑2 (MQ=255)
                                 taGGCATAAGTGAGGATATAGAGAACGAAGGCAACGGTAATACCGCTGATAATGTTcc                                                    >  1:1468136/1‑58 (MQ=255)
                                 taGGCATAAGTGAGGATATAGAGAACGAAGGCAACGGTAATACCGCTGATAATGTTcc                                                    >  1:4705894/1‑58 (MQ=255)
                                  aGGCATAGGTCAGGATATAGAGCACAAAGGCAATGGAAATGc                                                                   >  1:2967980/1‑42 (MQ=255)
                                  aGGCATAGGTCAGGATATAGAGCACAAAGGCAATGGAAATGCCGTTGAc                                                            <  1:2449244/49‑1 (MQ=255)
                                    gCATAGGTCAGGATATAGAGCACAAAGGCAATGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCa                                     >  1:3476297/1‑70 (MQ=255)
                                      aTAGGTCAGGATATAGAGCACAAAGGCAATGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCAAAt                                  <  1:5670630/71‑1 (MQ=255)
                                       tAGGTCAGGATATAGAGCACAAAGGCAATGGAAATGCCGTTGACCACGt                                                       <  1:3513886/49‑1 (MQ=255)
                                         ggTCAGGATATAGAGCACAAAGGCAATGGAAATGCCGTTGACCACGTTc                                                     >  1:4955361/1‑49 (MQ=255)
                                         ggTCAGGATATAGAGCACAAAGGCAATGGAAATGCCGTTGACCACGTTc                                                     >  1:2629588/1‑49 (MQ=255)
                                         ggTCAGGATATAGAGCACAAAGGCAATGGAAATGCCGTTGACCACGTTCCAGCCttt                                             <  1:1562379/57‑1 (MQ=255)
                                         ggTCAGGATATAGAGCACAAAGGCAATGGAAATGCCGTTGACAACGTTc                                                     >  1:5291231/1‑49 (MQ=255)
                                          gTCAGGATATAGAGCACAAAGGCAATGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCAAATCtt                               <  1:4258585/70‑1 (MQ=255)
                                            cAGGATATAGAGCACAAAGGCAATGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCCGCAAATCTTTg                             >  1:2796383/1‑70 (MQ=255)
                                             aGGATATAGAGAACGAAGGCAACGGTAATACCGCTGATAATGTTCCAGGTGTTACCGATTAAATCTTTGGt                           >  1:3723559/1‑71 (MQ=255)
                                              ggATATAGAGCACAAAGGCAATGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCAAATCTTTGGTg                          <  1:4305190/71‑1 (MQ=255)
                                               gATATAGAGCACAAAGGCAATGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCAAATCTTTGGTGa                         >  1:5392089/1‑71 (MQ=255)
                                               gATATAGAGCACAAAGGCAATGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCAAATCTTTGGTGa                         <  1:2813722/71‑1 (MQ=255)
                                                   taGAGCACAAAGGCAATGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCAAATCTTTGGTg                          <  1:841671/66‑1 (MQ=255)
                                                   taGAGCACAAAGGCAATGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCAAATCTTTGGTg                          >  1:1008746/1‑66 (MQ=255)
                                                   taGAGCACAAAGGCAATGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCAAATCTTTGGTGa                         <  1:5029024/67‑1 (MQ=255)
                                                     gagCACATAGGCAATGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCAAATCTTTGGTGa                         <  1:2824126/65‑1 (MQ=255)
                                                     gagCACAAAGGCAATGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCATATCttt                              <  1:11791/60‑1 (MQ=255)
                                                     gagCACAAAGGCAATGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCAAATCttt                              <  1:1146724/60‑1 (MQ=255)
                                                     gagCACAAAGGCAATGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCAAATCttt                              <  1:4053417/60‑1 (MQ=255)
                                                     gagCACAAAGGCAATGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCAAATCTTTGGTGATGgtg                    >  1:836607/1‑70 (MQ=255)
                                                       gCACAAAGGCAATGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCAAATCTTTgg                            >  1:4798413/1‑60 (MQ=255)
                                                        cacaAAGGCAATGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCAAATCTTTGGTGATGGTGTCaa                <  1:2050087/71‑1 (MQ=255)
                                                         acgaaGGCAACGGTAATACCGCTGATAATGTTCCAGGTGTTACCGATTAAATCTTTGGTGATGGTGTTaa                <  1:5010047/67‑1 (MQ=255)
                                                         acgaaGGCAACGGTAATACCGCTGATAATGTTCCAGGTGTTACCGATTAAATCTTTGGTGATGGTGTTaa                <  1:4131665/67‑1 (MQ=255)
                                                         acaAAGGCAATGGAAATGCCGTTGACCACGTTCCAGCCttt                                             <  1:2357421/41‑1 (MQ=255)
                                                         acaAAGGCAATGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCAAATCTTTGGTGATGGTGTCaa                <  1:3226932/70‑1 (MQ=255)
                                                          cgaaGGCAACGGTAATACCGCTGATAATGTTCCAGGTGTTACCGATTAAATCTTTGGTGATGGTGTTaaaa              >  1:1372428/3‑71 (MQ=255)
                                                          cgaaGGCAACGGTAATACCGCTGATAATGTTCCAGGTGTTACCGATTAAATCTTTGGTGATGGTGTTaaaa              <  1:223424/69‑1 (MQ=255)
                                                          cgaaGGCAACGGTAATACCGCTGATAATGTTCCAGGTGTTACCGATTAAATCTTTGGTGATGGTGTTaaaa              >  1:190574/3‑71 (MQ=255)
                                                          caAAGGCAATGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCAAATCTTTGGTGATg                       <  1:307056/62‑1 (MQ=255)
                                                          caAAGGCAATGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCAAATCTTTGGTGATGGTGTCaaaa              <  1:4942605/71‑1 (MQ=255)
                                                             aGGCAATGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCAAATc                                 <  1:1220998/49‑1 (MQ=255)
                                                             aGGCAATGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCAAATc                                 <  1:721850/49‑1 (MQ=255)
                                                             aGGCAATGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCAAATCTTTGGTGATGGTGTCAAAACTc           >  1:4489128/1‑71 (MQ=255)
                                                             aGGCAACGGTAATACCGCTGATAATGTTCCAGGTGTTACCGATTAAATCTTTGGTGATGgtgtta                 >  1:4137638/1‑63 (MQ=255)
                                                             aGGCAACGGTAATACCGCTGATAATGTTCCAGGTGTTACCGATTAAATCTTTGGTGATGGTGTTAAAACtg           <  1:3774747/71‑2 (MQ=255)
                                                              ggCAACGGTAATACCGCTGATAATGTTCCAGGTGTTACCGATTAAATCTTTGGTGATGGTGTTAAAACtgg          <  1:2852568/71‑3 (MQ=255)
                                                               gCAATGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCAAATCTTTGGTGa                         >  1:4735662/1‑55 (MQ=255)
                                                               gCAATGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCAAATCTTTGGTGa                         >  1:3868890/1‑55 (MQ=255)
                                                                 aaTGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCAAATCtt                               <  1:3966389/47‑1 (MQ=255)
                                                                 aaTGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCAAATCTTTGGt                           >  1:5439009/1‑51 (MQ=255)
                                                                 aaTGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCAAATCTTTGGt                           >  1:940966/1‑51 (MQ=255)
                                                                 aaTGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCAAATCTTTGGt                           >  1:5610506/1‑51 (MQ=255)
                                                                  aTGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCaaa                                   >  1:5349269/1‑42 (MQ=255)
                                                                  aTGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCaaa                                   >  1:1236361/1‑42 (MQ=255)
                                                                  aTGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCAAATCt                                <  1:3890396/45‑1 (MQ=255)
                                                                  aTGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCAAATCt                                <  1:2854481/45‑1 (MQ=255)
                                                                  aTGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCAAATCt                                <  1:4840014/45‑1 (MQ=255)
                                                                  aTGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCAAATCTTTgg                            <  1:1941406/49‑1 (MQ=255)
                                                                   tGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCAAATCtt                               >  1:644446/1‑45 (MQ=255)
                                                                   tGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCAAATCtt                               <  1:1311217/45‑1 (MQ=255)
                                                                   tGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCAAATCTTTg                             >  1:3599880/1‑47 (MQ=255)
                                                                   tGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCAAATCTTTGGt                           <  1:1357031/49‑1 (MQ=255)
                                                                    ggAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGc                                      >  1:3105797/1‑37 (MQ=255)
                                                                    ggAAATGCCGTTGACCACGTTCCAGCCTTTGCCAAGCAAATCttt                              >  1:1344116/1‑45 (MQ=255)
                                                                      aaaTGCCGTTGACCACGTTCCAGCCTTTGCCCAGCAAATCTTTGGTGATGGTGTCAAAACTCGAACCGAtt  >  1:2521635/1‑71 (MQ=255)
                                                                      |                                                                      
GTGTGATGCAGAATCGAACCACTGGCAGAAATATAGGCATAGGTCAGGATATAGAGCACAAAGGCAATGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCAAATCTTTGGTGATGGTGTCAAAACTCGAACCGATT  >  minE/2130555‑2130695

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A