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 1,933,624 T→A 29.5% P273P (CCA→CCT)  lysS ← lysine tRNA synthetase, constitutive

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,933,6240TA29.5% 247.7 / 125.6 156P273P (CCA→CCT) lysSlysine tRNA synthetase, constitutive
Reads supporting (aligned to +/- strand):  ref base T (56/54);  new base A (18/28);  total (74/82)
Fisher's exact test for biased strand distribution p-value = 2.19e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

Only 100 of 179 total aligned reads displayed.

GCGATTCGGTCAGCTCGATCAGATCTTTGTAATCTGCGTAAGCCATGTAGAGTTCCATCATGGTGAACTCTGGGTTATGACGTACGGAAATACCTTCGTTACGGAAGTTACGGTTGATTTCGAATACACGCTCGAAGCCAC  >  minE/1933554‑1933694
                                                                      |                                                                      
gCGATTCGGTCAGCTCGATCAGATCTTTGTAATCTGCGTAAGCCATGTAGAGTTCCATCATGGTGAActct                                                                        >  1:4744690/1‑71 (MQ=255)
 cGATTCGGTCAGCTCGATCAGATCTTTGTAATCTGCGTAAGCCATGTAGAGTTCCATCATGGTGAACTCTg                                                                       >  1:4254158/1‑71 (MQ=255)
   aTTCGGTCAGCTCGATCAGATCTTTGTAATCTGCGTAAGCCATGTAGAGTTCCATCATGGTGAACTCTgg                                                                      >  1:1752748/1‑70 (MQ=255)
      cGGTCAGCTCGATCAGATCTTTGTAATCTGCGTAAGCCATGTAGAGTTCCATCATGGTGAACTCTGGGTTa                                                                  >  1:724880/1‑71 (MQ=255)
      cGGTCAGCTCGATCAGATCTTTGTAATCTGCGTAAGCCATGTAGAGTTCCATCATGGTGAACTCTGGGTTa                                                                  >  1:524734/1‑71 (MQ=255)
       tgTCAGTTCAATCAAATCGTGGTAATCCGCATACGCCATGTAGAGTTCCATCATTGTGAACTCAGGATTAt                                                                 >  1:4743265/2‑71 (MQ=255)
        gTCAGCTCGATCAGATCTTTGTAATCTGCGTAAGCCATGTAGAGTTCCATCATGGTGAACTCTGGGTTATg                                                                <  1:658033/71‑1 (MQ=255)
         tCAGTTCAATCAAATAGTGGTAATCCGCATACGCCATGTAGAGTTCCATCATTGTGAACTCAGGATTa                                                                  <  1:3702415/68‑1 (MQ=255)
           aGCTCGATCAGATCTTTGTAATCTGCGTAAGCCATGTAGAGTTCCATCATGGTGAACTCTGGGTTATGACg                                                             >  1:1337695/1‑71 (MQ=255)
               cGATCAGATCTTTGTAATCTGCGTAAGCCATGTAGAGTTCCATCATGGTGAActct                                                                        <  1:290926/56‑1 (MQ=255)
               cGATCAGATCTTTGTAATCTGCGTAAGCCATGTAGAGTTCCATCATGGTGAActct                                                                        <  1:249314/56‑1 (MQ=255)
               cGATCAGATCTTTGTAATCTGCGTAAGCCATGTAGAGTTCCATCATGGTGAActct                                                                        <  1:3499983/56‑1 (MQ=255)
               cGATCAGATCTTTGTAATCTGCGTAAGCCATGTAGAGTTCCATCATGGTGAACTCTggg                                                                     >  1:4682924/1‑59 (MQ=255)
               cGATCAGATCTTTGTAATCTGCGTAAGCCATGTAGAGTTCAATCATGGTGAACTCTggg                                                                     >  1:2521287/1‑59 (MQ=255)
                gATCAGATCTTTGTAATCTGCGTAAGCCATGTAGAGTTCCATCATGGTGAACTCTGGGTTATGACGTAc                                                          <  1:4813837/69‑1 (MQ=255)
                gATCAGATCTTTGTAATCTGCGTAAGCCATGTAGAGTTCCATCATGGTGAACTCTGGGTTATGACGTAc                                                          <  1:2618209/69‑1 (MQ=255)
                  taaGATCTTTGTAATCTGCGTAAGCCATGTAGAGTTCCATCATGGTGAACTCTGGGTTATGACGTACGGa                                                       <  1:2749264/68‑1 (MQ=255)
                  tCAAATCGTGGTAATCCGCATACGCCATGTAGAGTTCCATCATTGTGAACTCAGGATTATGGCGAACAGa                                                       >  1:5617105/1‑70 (MQ=255)
                        cTTTGTAATCTGCGTAAGCCATGTAGAGTTCCATCATGGTGAACTCTGGGTTATGACGTACg                                                         >  1:3107546/1‑62 (MQ=255)
                         tttGTAATCTGCGTAAGCCATGTAGAGTTCCATCATGGTGAACTCTGGGTTATGACg                                                             <  1:5237807/57‑1 (MQ=255)
                         gtggTAATCCGCATACGCCATGTAGAGTTCCATCATTGTGAACTCAGGATTATGGCGAACAGAAATACCtt                                               >  1:5217119/4‑71 (MQ=255)
                         gtggTAATCCGCATACGCCATGTAGAGTTCCATCATTGTGAACTCAGGATTATGGCGAACAGAAATACCtt                                               >  1:4159908/4‑71 (MQ=255)
                         gtggTAATCCGCATACGCCATGTAGAGTTCCATCATTGTGAACTCAGGATTATGGCGAACAGAAATACCtt                                               >  1:2696559/4‑71 (MQ=255)
                          ttGTAATCTGCGTAAGCCATGTAGAGTTCCATCATGGTGAACTCTGGGTTa                                                                  >  1:320873/1‑51 (MQ=255)
                          ttGTAATCTGCGTAAGCCATGTAGAGTTCCATCATGGTGAACTCTGGGTTa                                                                  >  1:110065/1‑51 (MQ=255)
                           tGTAATCTGCGTAAGCCATGTAGAGTTCCATCATGGTGAACTCTGGGTTATGACGTACGGAAATACCtt                                               <  1:2841/69‑1 (MQ=255)
                           tGTAATCTGCGTAAGCCATGTAGAGTTCCATCATGGTGAACTCTGGGTTATGACGTACGGAAATACCTTCg                                             >  1:4408375/1‑71 (MQ=255)
                             tAATCCGCATACGCCATGTAGAGTTCCATCATTGTGAACTCAGGATTATGGCGAACAGAAATACCTTca                                             <  1:4238562/69‑2 (MQ=255)
                               aTCCGCATACGCCATGTAGAGTTCCATCATTGTGAACTCAGGATTATGGCGAACAGaaa                                                     >  1:3950377/1‑59 (MQ=255)
                               aTCCGCATACGCCATGTAGAGTTACATCATTGTGAACTCAGGATTATGGCGAACAGaa                                                      >  1:4041847/1‑58 (MQ=255)
                                  tGCGTAAGCCATGTAGAGTTCCATCATGGTGAACTCTGGGTTATGACGTACGGAAATACCTTCGTTACgg                                       >  1:3010245/1‑70 (MQ=255)
                                  tGCGTAAGCCATGTAGAGTTCCATCATGGTGAACTCTGGGTTATGACGTACGGAAATACCTTCGTTACgg                                       >  1:46491/1‑70 (MQ=255)
                                    cGTAAGCCATGTAGAGTTCCATCATGGTGAACTCTGGGTTATGACGTACGGAAATACCTTCGTTACGGa                                      <  1:2944428/69‑1 (MQ=255)
                                      tacgCCATGTAGAGTTCCATCATTGTGAACTCAGGATTATGGCGAACAGAAATACCTTCATTACGGAAGtt                                  <  1:4557750/68‑1 (MQ=255)
                                       acgCCATGTAGAGTTCCATCATTGTGAACTCAGGATTATGGCGAACAGa                                                       <  1:3607038/47‑1 (MQ=255)
                                       aaGCCATGTAGATTTCCATCATGGTGAACTCTGGGTTATGACGTACGGAAATACCTTCGTTACGGAAGTTa                                 >  1:3969084/1‑71 (MQ=255)
                                       aaGCCATGTAGAGTTCCATCATGGTGAACTCTGGGTTATGACGTACGGAAATACCTTCGTTACGGAAGTTa                                 >  1:2642069/1‑71 (MQ=255)
                                        cgCCATGTAGAGTTCCATCATTGTTAACTCAGGATTATTGCGAACAGAAATACCTTCATTACTGAAGTTa                                 <  1:5536968/69‑1 (MQ=255)
                                        cgCCATGTAGAGTTCCATCATTGTGAACTCAGGATTATGGCGAACAGAAATACCTTCATTACGGAAGTTa                                 <  1:2043105/69‑1 (MQ=255)
                                        cgCCATGTAGAGTTCCATCATTGTGAACTCAGGATTATGGCGAACAGAAATACCTTCATTACGGAAGTTa                                 <  1:1962743/69‑1 (MQ=255)
                                        aGCCATGTAGAGTTCCATCATGGTGAACTCTGGGTTATGACGTACGGAAATa                                                   >  1:1549854/1‑52 (MQ=255)
                                        aGCCATGTAGAGTTCCATCATGGTGAACTCTGGGTTATGACGTACGGAAATACCTTCGTTACGGAAGTTa                                 <  1:125228/70‑1 (MQ=255)
                                        aGCCATGTAGAGTTCCATCATGGTGAACTCTGGGTTATGACGTACGGAAATACCTTCGTTACGGAAGTTAc                                <  1:2409599/71‑1 (MQ=255)
                                        aGCCATGTAGAGTTCCATCATGGTGAACTCTGGGTTATGACGTACGGAAATACCTTCGTTACGGAAGTTAc                                <  1:166163/71‑1 (MQ=255)
                                        aGCCATGTAGAGTTCCATCATGGTGAACTCTGGGTTATGACGTACGGAAATACCTTCGTTACGGAAGTTAc                                <  1:489138/71‑1 (MQ=255)
                                        aGCCATGTAGAGTTCCATCATGGTGAACTCTGGGTTATGACGTACGGAAATACCTTCGTTACGGAAGTTAc                                >  1:4836025/1‑71 (MQ=255)
                                         gCCATGTAGAGTTCCATCATTGTGAACTCAGGATTATGGCGAACAGAAATACCTTCATTACGGAAGTTACg                               >  1:5644200/1‑71 (MQ=255)
                                         gCCATGTAGAGTTCCATCATTGTGAACTCAGGATTATGGCGAACAGAAATACCTTCATTACGGAAGTTACg                               >  1:4784605/1‑71 (MQ=255)
                                         gCCATGTAGAGTTCCATCATTGTGAACTCAGGATTATGGCGAACAGAAATACCTTCATTACGGAAGTTACg                               >  1:1069434/1‑71 (MQ=255)
                                           cATGTAGAGTTCCATCATGGTGAACTCTGGGTTATGACGTACGGAAATACCTTCGTTACGGAAGtt                                  <  1:3032491/66‑1 (MQ=255)
                                            aTGTAGAGTTCCATCATGGTGAACTCTGGGTTATGACGTACGGAAATACCTTCGTTACGGAAGTTACGGtt                            <  1:165428/71‑1 (MQ=255)
                                             tGTAGAGTTCCATCATGGTGAACTCTGGGTTATGACGTACGGAAATACCTTCGTTa                                          >  1:3692779/1‑56 (MQ=255)
                                             tGTAGAGTTCCATCATGGTGAACTCTGGGTTATGACGTACGGAAATACCTTCGTTACGGa                                      <  1:4393245/60‑1 (MQ=255)
                                              gTAGAGTTCCATCATTGTGAACTCAGGATTATGGCGAACAGa                                                       <  1:3789488/42‑1 (MQ=16)
                                              gTAGAGTTCCATCATGGTGAACTCTGGGTTATGACGTACGGaaa                                                     >  1:5561247/1‑44 (MQ=255)
                                              gTAGAGTTCCATCATGGTGAACTCTGGGTTATGACGTACGGaaa                                                     >  1:4270924/1‑44 (MQ=255)
                                               tAGAGTTCCATCATTGTGAACTCAGGATTATGGCGAACAGaaa                                                     >  1:1369690/1‑43 (MQ=16)
                                               tAGAGTTCCATCATGGTGAACTCTGGGTTATGACg                                                             >  1:880187/1‑35 (MQ=255)
                                               tAGAGTTCCATCATGGTGAACTCTGGGTTATGACGTACGGaaa                                                     >  1:4208479/1‑43 (MQ=255)
                                               tAGAGTTCCATCATGGTGAACTCTGGGTTATGACGTACGGAAATAcc                                                 <  1:1531179/47‑1 (MQ=255)
                                               tAGAGTTCCATCATGGTGAACTCTGGGTTATGACGTACGGAAATACCTTCGTTACGGAAGTTACGGTTGAt                         >  1:5302943/1‑71 (MQ=255)
                                               tAGAGTTCCATCATGGTGAACTCTGGGTTATGACGTACGGAAATACCTTCGTTACGGAAGTTACGGTTGAt                         >  1:3599301/1‑71 (MQ=255)
                                               tAGAGTTCCATCATGGTGAACTCTGGGTTATGACGTACGGAAATACCTTCGTTACGGAAGTTACGGTTGAt                         >  1:176459/1‑71 (MQ=255)
                                               tAGAGTTCCATCATGGTGAACTCTGGGTTATGACGTACGGAAATACCTTCGTTACGGAAGTTACGGTTGAt                         >  1:1807225/1‑71 (MQ=255)
                                                 gagTTCCATCATGGTGAACTCTGGGTTATGACGTACGGAAATACCtt                                               >  1:1417008/1‑47 (MQ=255)
                                                 gagTTCCATCATGGTGAACTCTGGGTTATGACGTACGGAAATACCtt                                               >  1:3508873/1‑47 (MQ=255)
                                                 gagTTCCATCATGGTGAACTCTGGGTTATGACGTACGGAAATACCt                                                >  1:5110416/1‑46 (MQ=255)
                                                  agTTCCATCATGGTGAACTCTGGGTTATGACGTACGGAAATACCTTCGTTACGGAAGTTACGGTTGATTTc                      >  1:565703/1‑71 (MQ=255)
                                                   gTTCCATCATGGTGAACTCTGGGTTATGACGTACGGAAATACCTTCGTTACGGAAGTTACGGTTGATTTCg                     <  1:3840340/71‑1 (MQ=255)
                                                     tCCATCATGGTGAACTATGGGTTATGACGTACGGAAATACCTTCGtt                                           <  1:725456/47‑1 (MQ=255)
                                                      ccATCATTGTGAACTCAGGATTATGGCGAACAGAAATACCTTCATTACGGAAGTTACGGTTGATTTCGaa                   >  1:194962/1‑70 (MQ=255)
                                                      ccATCATGGTGAACTCTGGGTTATGACGTACGGAAATACCTTCGTTACGGaa                                     >  1:4123391/1‑52 (MQ=255)
                                                      ccATCATGGTGAACTCTGGGTTATGACGTACGGAAATACCTTCGTTACGGaa                                     >  1:1003256/1‑52 (MQ=255)
                                                      ccATCATGGTGAACTCTGGGTTATGACGTACGGAAATACCTTCGTTACGGAAGTTACGGTTGa                          >  1:3729672/1‑63 (MQ=255)
                                                      ccATCATGGTGAACTCTGGGTTATGACGTACGGAAATACCTTCGTTACGGAAGTTACGGTTGAttt                       >  1:2290000/1‑66 (MQ=255)
                                                      acatcatGGTGAACTCTGGGTTATGACGTACGGAAATACCTTCGTTACGGaa                                     >  1:2891802/2‑52 (MQ=255)
                                                       catcatTGTGAACTCAGGATTATGGCGAACAGAAATACCTTCATTACGGAAGtt                                  <  1:4010804/54‑1 (MQ=255)
                                                       catcatTGTGAACTCAGGATTATGGCGAACAGAAATACCTTCATTACGGAAGTTACGGtt                            <  1:1451763/60‑1 (MQ=255)
                                                       catcatGGTGAACTCTGGGTTATGACGTACGGAAATACCTTCGTTACGGAAGTTACGGTTGa                          <  1:4511490/62‑1 (MQ=255)
                                                        atcatTGTGAACTCAGGATTATGGCGAACAGAAATACCTTCATTACGGAAGTTACGGTTGAt                         <  1:5451050/62‑1 (MQ=255)
                                                         tcatTGTGAACTCAGGATTATGGCGAACAGAAATACCTTCATTACGGAAGTTACGGTTGATTTCGAATacc               >  1:1618597/1‑70 (MQ=255)
                                                         tcatGGTGAACTCTGGGTTATGACGTACGGAAATACCTTCGTTACGGAAGTTACGGTTGAt                         <  1:2115306/61‑1 (MQ=255)
                                                          catGGTGAACTCTGGGTTATGACGTACGGAAATACCTTCGTTACGGAAGTTACGGTTGATTTCGAATacac              >  1:336618/1‑71 (MQ=255)
                                                             ggTGAACTCTGGGTTATGACGTACGGAAATACCTTCGTTACGGAAGTTACGGTTGATTTCGa                    <  1:2793424/62‑1 (MQ=255)
                                                             ggTGAACTCTGGGTTATGACGTACGGAAATACCTTCGTTACGGAAGTTACGGTTGATTTCGAATACACg             >  1:780594/1‑69 (MQ=255)
                                                              gTGAACTCTGGGTTATGACGTACGGAAATACCTTCGTTACGGAAGTTACGGTTGATTTCGAATACACGCt           <  1:675221/70‑1 (MQ=255)
                                                               tGAACTCTGGGTTATGACGTACGGAAATACCTTCGTTACGGAAGTTACGGTTGATTTCGAATACACGCTCg         <  1:1146341/71‑1 (MQ=255)
                                                               tGAACTCAGGATTATGGCGAACAGAAATACCTTCATTACGGAAGTTACGGTTGATTTCGAATACCCGTTca         <  1:554714/71‑2 (MQ=255)
                                                                 aaCTCTGGGTTATGACGTACGGAAATACCTTCGTTACGGAAGTTACGGtt                            <  1:1251588/50‑1 (MQ=255)
                                                                 aaCTCTGGGTTATGACGTACGGAAATACCTTCGTTACGGAAGTTACGGtt                            <  1:91075/50‑1 (MQ=255)
                                                                 aaCTCTGGGTTATGACGTACGGAAATACCTTCGTTACGGAAGTTACGGtt                            <  1:5358803/50‑1 (MQ=255)
                                                                 aaCTCAGGATTATGGCGAACAGAAATACCTTCATTACGGAAGTTACGGTTGATTTCGAATACCCGTTcaa        <  1:2987779/70‑3 (MQ=255)
                                                                   ctctGGGTTATGACGTACGGAAATACCTTCGTTACGGAAGTTACGGTTGATTTCGAATACACGCTCGAAGc     <  1:4084731/71‑1 (MQ=255)
                                                                      tGGGTTATGACGTACGGAAATACCTTCGTTACGGAAGTTACg                               <  1:5368982/42‑1 (MQ=255)
                                                                      tGGGTTATGACGTACGGAAATACCTTCGTTACGGAAGTTACGGTTGATTTCGAATACACGCTCGa        <  1:4923416/65‑1 (MQ=255)
                                                                      tGGGTTATGACGTACGGAAATACCTTCGTTACGGAAGTTACGGTTGATTTCGAATACACGCTCGa        <  1:4519719/65‑1 (MQ=255)
                                                                      tGGGTTATGACGTACGGAAATACCTTCGTTACGGAAGTTACGGTTGATTTCGAATACACGCTCGAAGccac  >  1:5437985/1‑71 (MQ=255)
                                                                      tGGGTTATGACGTACGGAAATACCTTCGTTACGGAAGTTACGGTTGATTTCGAATACACGCTCGAAGccac  >  1:4228905/1‑71 (MQ=255)
                                                                      tGGGTTATGACGTACGGAAATACCTTCGTTACGGAAGTTACGGTTGATTTCGAATACACGCTCGAAGc     <  1:1602887/68‑1 (MQ=255)
                                                                      tGGGTTATGACGTACGGAAATACCTTCGTTACGGAAGTTAAGGTTGATTTCGAATACACGCTCGAAGccac  >  1:2157608/1‑71 (MQ=255)
                                                                      |                                                                      
GCGATTCGGTCAGCTCGATCAGATCTTTGTAATCTGCGTAAGCCATGTAGAGTTCCATCATGGTGAACTCTGGGTTATGACGTACGGAAATACCTTCGTTACGGAAGTTACGGTTGATTTCGAATACACGCTCGAAGCCAC  >  minE/1933554‑1933694

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