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 2,130,633 T→C 20.5% N91S (AAC→AGC)  mtr ← tryptophan transporter of high affinity

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,130,6330TC20.5% 276.5 / 65.7 141N91S (AAC→AGC) mtrtryptophan transporter of high affinity
Reads supporting (aligned to +/- strand):  ref base T (54/58);  new base C (14/15);  total (68/73)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.85e-01

Only 100 of 145 total aligned reads displayed.

AGAATCGAACCACTGGCAGAAATATAGGCATAGGTCAGGATATAGAGCACAAAGGCAATGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCAAATCTTTGGTGATGGTGTCAAAACTCGAACCGATTCTGT  >  minE/2130564‑2130699
                                                                     |                                                                  
aGAATCGAACCACTGGCAGAAATATAGGCATAGGTCAGGATATAGAGCACAAAGGCAATGGAAATGCCGtt                                                                   <  1:2573442/71‑1 (MQ=255)
 gAATCGAACCACTGGCAGAAATATAGGCATAGGTCAGGATATAGAGCACAAAGGCAATGGAAATGCCGtt                                                                   >  1:4628389/1‑70 (MQ=255)
   aTCGCACCATTAGCAGAGATATAGGCATAAGTGAGGATATAGAGAACGAAGGCAACGGTAATACCGCTGat                                                                <  1:1718479/71‑2 (MQ=255)
   aTCGCACCATTAGCAGAGATATAGGCATAAGTGAGGATATAGAGAACGAAGGCAACGGTAATACCGCTGat                                                                <  1:4250176/71‑2 (MQ=255)
   aTCGCACCATTAGCAGAGATATAGGCATAAGTGAGGATATAGAGAACGAAGGCAACGGTAATACCGCTGat                                                                <  1:5186317/71‑2 (MQ=255)
   aTCGCACCATTAGCAGAGATATAGGCATAAGTGAGGATATAGAGAACGAAGGCAACGGTAATACCGCTGat                                                                <  1:4173012/71‑2 (MQ=255)
    tCGAACCACTGGCAGAAATATAGGCATAGGTCAGGATATAGAGCACAAAGGCAATGGAAATGCCGTTGAc                                                                >  1:2605545/1‑70 (MQ=255)
    tCGAACCACTGGCAGAAATATAGGCATAGGTCAGGATATAGAGCACAAAGGCAATGGAAATGCCGTTGAc                                                                >  1:4458215/1‑70 (MQ=255)
      gAACCACTGGCAGAAATATAGGCATAGGTCAGGATATAGAGCACAAAGGCAATGGAAATGCCGTTGACCa                                                              >  1:1514809/1‑70 (MQ=255)
      gAACCACTGGCAGAAATATAGGCATAGGTCAGGATATAGAGCACAAAGGCAATGGAAATGCCGTTGACCAc                                                             >  1:1087905/1‑71 (MQ=255)
         ccACTGGCAGAAATATAGGCATAGGTCAGGATATAGAGCACAAAGGCAATGGAAATGCCGTTGACCACGtt                                                          <  1:648042/71‑1 (MQ=255)
          cACTGGCAGAAATATAGGCATAGGTCAGGATATAGAGCACAAAGGCAATGGAAATGCCGTTGACCACGTTc                                                         <  1:4121138/71‑1 (MQ=255)
            cTGGCAGAAATATAGGCATAGGTCAGGATATAGAGCACAAAGGCAATGGAAATGCCGTTGACCa                                                              >  1:1605069/1‑64 (MQ=255)
            cTGGCAGAAATATAGGCATAGGTCAGGATATAGAGCACAAAGGCAATGGAAATGCCGTTGACCACGt                                                           <  1:2089049/67‑1 (MQ=255)
            cTGGCAGAAATATAGGCATAGGTCAGGATATAGAGCACAAAGGCAATGGAAATGCCGTTGACCACGt                                                           <  1:1466945/67‑1 (MQ=255)
              ggCAGAAATATAGGCATAGGTCAGGATATAGAGCACAAAGGCAATGGAAATGCCGTTGACCACGTTCCAGc                                                     >  1:4870493/1‑71 (MQ=255)
              agCAGAGATATAGGCATAAGTGAGGATATAGAGAACGAAGGCAACGGTAATACCGCTGa                                                                 <  1:1761793/58‑1 (MQ=255)
               gCAGAGATATAGGCATAAGTGAGGATATAGAGAACGAAGGCAACGGTAATACCGCTGATAATGTTCCAgg                                                     >  1:3911616/1‑69 (MQ=255)
                   agatatAGGCATAAGTGAGGATATAGAGAACGAAGGCAACGGTAATACCGCTGATAATGTTcc                                                        >  1:4209174/3‑63 (MQ=255)
                   agatatAGGCATAAGTGAGGATATAGAGAACGAAGGCAACGGTAATACCGCTGATAATGTTcc                                                        >  1:2501159/3‑63 (MQ=255)
                   agatatAGGCATAAGTGAGGATATAGAGAACGAAGGCAACGGTAATACCGCTGATAATGTTcc                                                        >  1:5092420/3‑63 (MQ=255)
                   agatatAGGCATAAGTGAGGATATAGAGAACGAAGGCAACGGTAATACCGCTGATAATGTTcc                                                        >  1:2284749/3‑63 (MQ=255)
                   agatatAGGCATAAGTGAGGATATAAAGAACGAAGGCAACGGTAATACCGCTGATAATGTTcc                                                        >  1:5638411/3‑63 (MQ=255)
                     atatAGGCATAGGTCAGGATATAGAGCACAAAGGCAATGGAAATGCCGTTGACCACGTTCCa                                                       >  1:1084562/1‑62 (MQ=255)
                     atatAGGCATAGGTCAGGATATAGAGCACAAAGGCAATGGAAATGCCGTTGACCACGTTCCa                                                       >  1:2791634/1‑62 (MQ=255)
                     atatAGGCATAGGTCAGGATATAGAGCACAAAGGCAATGGAAATGCCGTTGACCACGTTCCAGCCTTTGcc                                              <  1:3590723/71‑1 (MQ=255)
                     atatAGGCATAGGTCAGGATATAGAGCACAAAGGCAATGGAAATGCCGTTGACCACGTTCCAGCCTTTGcc                                              >  1:1800618/1‑71 (MQ=255)
                      tataGGCATAGGTCAGGATATAGAGCACAAAGGCAATGGAAATGCCGTTGACCACGTTCCAGCCTTTGccc                                             <  1:2750719/71‑1 (MQ=255)
                       ataGGCATAGGTCAGGATATAGAGCACAAAGGCAATGGAAATGCCGTTGACCACGTTCCAGCCTTTGccc                                             <  1:3340983/70‑1 (MQ=255)
                       ataGGCATAGGTCAGGATATAGAGCACAAAGGCAATGGAAATGCCGTTGACCACGTTCCAGCCTTTGcc                                              <  1:5230412/69‑1 (MQ=255)
                        taGGCATAAGTGAGGATATAGAGAACGAAGGCAACGGTAATACCGCTGATAATGTTcc                                                        >  1:4705894/1‑58 (MQ=255)
                         aGGCATAGGTCAGGATATAGAGCACAAAGGCAATGGAAATGCCGTTGAc                                                                <  1:2449244/49‑1 (MQ=255)
                           gCATAGGTCAGGATATAGAGCACAAAGGCAATGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCa                                         >  1:2994315/1‑70 (MQ=255)
                           gCATAGGTCAGGATATAGAGCACAAAGGCAATGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCa                                         >  1:3476297/1‑70 (MQ=255)
                              tAGGTCAGGATATAGAGCACAAAGGCAATGGAAATGCCGTTGACCACGt                                                           <  1:3513886/49‑1 (MQ=255)
                              tAGGTCAGGATATAGAGCACAAAGGCAATGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCAAATc                                     >  1:389185/1‑71 (MQ=255)
                               aGGTCAGGATATAGAGCACAAAGGCGATGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCAAATCt                                    >  1:2905092/1‑71 (MQ=255)
                                ggTCAGGATATAGAGCACAAAGGCAATGGAAATGCCGTTGACCACGTTc                                                         >  1:4955361/1‑49 (MQ=255)
                                ggTCAGGATATAGAGCACAAAGGCAATGGAAATGCCGTTGACCACGTTCCAGCCttt                                                 <  1:1562379/57‑1 (MQ=255)
                                ggTCAGGATATAGAGCACAAAGGCAATGGAAATGCCGTTGACAACGTTc                                                         >  1:5291231/1‑49 (MQ=255)
                                   cAGGATATAGAGCACAAAGGCAATGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCCGCAAATCTTTg                                 >  1:2796383/1‑70 (MQ=255)
                                    aGGATATAGAGAACGAAGGCAACGGTAATACCGCTGATAATGTTCCAGGTGTTACCGATTAAATCTTTGGt                               >  1:3723559/1‑71 (MQ=255)
                                     ggATATAGAGCACAAAGGCAATGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCAAATCTTTGGTg                              <  1:4305190/71‑1 (MQ=255)
                                      gATATAGAGCACAAAGGCAATGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCAAATCTTTGGTGa                             <  1:2813722/71‑1 (MQ=255)
                                      gATATAGAGCACAAAGGCAATGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCAAATCTTTGGTGa                             >  1:5392089/1‑71 (MQ=255)
                                      gATATAGAGAACGAAGGCAACGGTAATACCGCTGATAATGTTCCAGGTGTTACCGATTAAATCTTTGGTGa                             >  1:3970433/1‑71 (MQ=255)
                                       atatAGAGCACAAAGGCAATGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCAAATCTTTGGTGAt                            <  1:2089740/71‑1 (MQ=255)
                                          taGAGCACAAAGGCAATGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCAAATCTTTGGTg                              >  1:1008746/1‑66 (MQ=255)
                                          taGAGCACAAAGGCAATGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCAAATCTTTGGTGa                             <  1:5022463/67‑1 (MQ=255)
                                          taGAGCACAAAGGCAATGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCAAATCTTTGGTGa                             <  1:3855934/67‑1 (MQ=255)
                                            gagCACATAGGCAATGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCAAATCTTTGGTGa                             <  1:2824126/65‑1 (MQ=255)
                                            gagCACAAAGGCAATGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCATATCttt                                  <  1:11791/60‑1 (MQ=255)
                                            gagCACAAAGGCAATGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCAAATCttt                                  <  1:1267016/60‑1 (MQ=255)
                                            gagCACAAAGGCAATGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCAAATCTTTGGTGATGgtg                        >  1:836607/1‑70 (MQ=255)
                                              gCACAAAGGCAATGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCAAATCTTTgg                                >  1:4798413/1‑60 (MQ=255)
                                               cacaAAGGCAATGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCAAATCTTTGGTGATGGTGTCaa                    <  1:3111314/71‑1 (MQ=255)
                                               cacaAAGGCAATGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCAAATCTTTGGTGATGGTGTCaa                    <  1:2050087/71‑1 (MQ=255)
                                               cacaAAGGCAATGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCAAATCTTTGGTGATGGTGTCaa                    <  1:4613688/71‑1 (MQ=255)
                                                acgaaGGCAACGGTAATACCGCTGATAATGTTCCAGGTGTTACCGATTAAATCTTTGGTGATGGTGTTaa                    <  1:4131665/67‑1 (MQ=255)
                                                acgaaGGCAACGGTAATACCGCTGATAATGTTCCAGGTGTTACCGATTAAATCTTTGGTGATGGTGTTaa                    <  1:5535236/67‑1 (MQ=255)
                                                acgaaGGCAACGGTAATACCGCTGATAATGTTCCAGGTGTTACCGATTAAATCTTTGGTGATGGTGTTaa                    <  1:5010047/67‑1 (MQ=255)
                                                acaAAGGCAATGGAAATGCCGTTGACCACGTTCCAGCCttt                                                 <  1:2357421/41‑1 (MQ=255)
                                                acaAAGGCAATGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCAAATCTTTGGTGATGGTGTCaa                    <  1:3226932/70‑1 (MQ=255)
                                                 cgaaGGCAACGGTAATACCGCTGATAATGTTCCAGGTGTTACCGATTAAATCTTTGGTGATGGTGTTaaaa                  <  1:223424/69‑1 (MQ=255)
                                                 cgaaGGCAACGGTAATACCGCTGATAATGTTCCAGGTGTTACCGATTAAATCTTTGGTGATGGTGTTaaaa                  >  1:1372428/3‑71 (MQ=255)
                                                 caAAGGCAATGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCAAATCTTTGGTGATg                           <  1:307056/62‑1 (MQ=255)
                                                 caAAGGCAATGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCAAATCTTTGGTGATGGTGTCaaaa                  <  1:4942605/71‑1 (MQ=255)
                                                   aaGGCAATGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCAAATCTTTGGTGATGGTGTCaaaa                  >  1:2756128/1‑69 (MQ=255)
                                                    aGGCAATGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCAAAt                                      >  1:5668755/1‑48 (MQ=255)
                                                    aGGCAATGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCAAATc                                     <  1:4152227/49‑1 (MQ=255)
                                                    aGGCAATGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCAAATc                                     <  1:1220998/49‑1 (MQ=255)
                                                    aGGCAATGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCAAATc                                     <  1:721850/49‑1 (MQ=255)
                                                    aGGCAATGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCAAATCTTTGGTGATGGTGTCAAAACTc               >  1:4489128/1‑71 (MQ=255)
                                                    aGGCAATGGAAATGCCGTTAACCACGTTCCAGCCTTTGCCCAGCAAAt                                      >  1:2848161/1‑48 (MQ=255)
                                                    aGGCAACGGTAATACCGCTGATAATGTTCCAGGTGTTACCGATTAAATCTTTGGTGATGGTGTTAAAACtg               <  1:2681888/71‑2 (MQ=255)
                                                      gCAATGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCAAATCTTTg                                 >  1:2372887/1‑51 (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)
                                                         aTGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCaaa                                       >  1:5349269/1‑42 (MQ=255)
                                                         aTGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCaaa                                       >  1:1236361/1‑42 (MQ=255)
                                                         aTGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCAAATCt                                    <  1:2854481/45‑1 (MQ=255)
                                                         aTGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCAAATCt                                    <  1:4840014/45‑1 (MQ=255)
                                                         aTGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCAAATCTTTgg                                <  1:1796894/49‑1 (MQ=255)
                                                         aTGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCAAATCTTTgg                                <  1:1938430/49‑1 (MQ=255)
                                                         aTGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCAAATCTTTgg                                <  1:1941406/49‑1 (MQ=255)
                                                          tGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCAAATCtt                                   <  1:1311217/45‑1 (MQ=255)
                                                          tGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCAAATCtt                                   >  1:644446/1‑45 (MQ=255)
                                                          tGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCAAATCTTTg                                 >  1:3599880/1‑47 (MQ=255)
                                                          tGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCAAATCTTTGGt                               <  1:1357031/49‑1 (MQ=255)
                                                           ggAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGc                                          >  1:883130/1‑37 (MQ=255)
                                                           ggAAATGCCGTTGACCACGTTCCAGCCTTTGCCAAGCAAATCttt                                  >  1:1344116/1‑45 (MQ=255)
                                                             aaaTGCCGTTGACCACGTTCCAGCCTTTGCCCAGCAAATCTTTGGTGATGGTGTCAAAACTCGAACCGAtt      >  1:2521635/1‑71 (MQ=255)
                                                                tGCCGTTGACCACGTTCCAGCCTTTGCCCAGCAAATCTTTGGTGATGGTGTCAAAACTCGAACCGATTc     <  1:1520045/69‑1 (MQ=255)
                                                                  ccGTTGACCACGTTCCAGCCTTTGCCCAGCAAATCTTTGGTGATGGTGTCAAAACTCGAACCGATTCTGt  >  1:5087710/1‑70 (MQ=255)
                                                                   cGTTGACCACGTTCCAGCCTTTGCCCAGCAAATCTTTGGTGATGGTGTCaa                    <  1:268737/51‑1 (MQ=255)
                                                                    gTTGACCACGTTCCAGCCTTTGCCCAGCAAATCTTTGGTGATGGTGTCaaaa                  >  1:3957565/1‑52 (MQ=255)
                                                                    gTTGACCACGTTCCAGCCTTTGCCCAGCAAATCTTTGGTGATGGTGTCAAAACTCGAAcc          <  1:3655996/60‑1 (MQ=255)
                                                                     |                                                                  
AGAATCGAACCACTGGCAGAAATATAGGCATAGGTCAGGATATAGAGCACAAAGGCAATGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCAAATCTTTGGTGATGGTGTCAAAACTCGAACCGATTCTGT  >  minE/2130564‑2130699

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