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 832,322 G→A 35.7% T260T (ACG→ACA)  narG → nitrate reductase 1, alpha subunit

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE832,3220GA35.7% 94.5 / 88.0 98T260T (ACG→ACA) narGnitrate reductase 1, alpha subunit
Reads supporting (aligned to +/- strand):  ref base G (35/28);  new base A (16/19);  total (51/47)
Fisher's exact test for biased strand distribution p-value = 4.02e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

Only 100 of 102 total aligned reads displayed.

ACGTACCGGAATCTGCTGACTGGTACAACTCCAGCTACATCATCGCCTGGGGGTCAAACGTGCCGCAGACGCGTACCCCGGATGCTCACTTCTTTACTGAAGTGCGTTACAAAGGGACCAAAACTGTTGCCGTCACACCA  >  minE/832252‑832391
                                                                      |                                                                     
aCGTACCGGAATCTGCTGACTGGTACAACTCCAGCTACATCATCGCCTGGGGGTCAAACGTGCCGCAGAcg                                                                       >  1:2852621/1‑71 (MQ=255)
     ccGGAATCTGCTGACTGGTACAACTCCAGCTACATCATCGCCTGGGGGTCAAACGTGCCGCAGACGCGTAc                                                                  >  1:4827136/1‑71 (MQ=255)
     ccGGAATCTGCCGACTGGTATAACTCCAGCTACATCATCGCCTGGGGGTCTAACGTACCGCAGACACGTAc                                                                  >  1:2828340/1‑71 (MQ=255)
      cGGAATCTGCTGACTGGTACAACTCCAGCTACATCATCGCCTGGGGGTCAAACGTGCCGCAGAcgcg                                                                     <  1:3832576/67‑1 (MQ=255)
        gAATCTGCTGACTGGTACAACTCCAGCTACATCATCGCCTGGGGGTCAAACGTGCCGCAGACGCGTAcccc                                                               >  1:676253/1‑71 (MQ=255)
        gAATCTGCTGACTGGTACAACTCCAGCTACATCATCGCCTGGGGGTCAAACGTGCCGCAGACGCGTAcccc                                                               >  1:2135068/1‑71 (MQ=255)
        gAATCTGCTGACTGGTACAACTCCAGCTACATCATCGCCTGGGGGTCAAACGTGCCGCAGACGCGTAcc                                                                 >  1:3576965/1‑69 (MQ=255)
        gAATCTGCCGACTGGTATAACTCCAGCTACATCATCGCCTGGGGGTCTAACGTACCGCAGACACGTAcgcc                                                               <  1:878330/71‑1 (MQ=255)
         aaTCTGCTGACTGGTACAACTCCAGCTACATCATCGCCTGGGGGTCAAACGTGCCGCAGACGCGt                                                                    <  1:5454331/65‑1 (MQ=255)
         aaTCTGCTGACTGGTACAACTCCAGCTACATCATCGCCTGGGGGTCAAACGTGCCGCAGACGCGt                                                                    <  1:2089654/65‑1 (MQ=255)
          aTCTGCTGACTGGTACAACTCCAGCTACATCATCGCCTGGGGGTCAAACGTGCCGCAGACGCGTACCCCgg                                                             <  1:3040704/71‑1 (MQ=255)
           tCTGCTGACTGGTACAACTCCAGCTACATCATCGCCTGGGGGTCAAACGTGCCGCAGACGCGTAc                                                                  >  1:166102/1‑65 (MQ=255)
           tCTGCTGACTGGTACAACTCCAGCTACATCATCGCCTGGGGGTCAAACGTGCCGCAGACGCGTAc                                                                  >  1:127842/1‑65 (MQ=255)
           tCTGCTGACTGGTACAACTCCAGCTACATCATCGCCTGGGGGTCAAACGTGCCGCAGACGCGTAc                                                                  >  1:240491/1‑65 (MQ=255)
            ctgctgACTGGTACAACTCCAGCTACATCATCGCCTGGGGGTCAAACGTGCCGCAGACGCGTACCCCGGAt                                                           >  1:2694472/1‑71 (MQ=255)
             tgctgACTGGTACAACTCCAGCTACATCATCGCCTGGGGGTCAAACGTGCCGCAGACGCGTACCCCGGATg                                                          >  1:4384016/1‑71 (MQ=255)
             tgccgACTGGTATAACTCCAGCTACATCATCGCCTGGGGGTCTAACGTACCGCAGACACGTACGCCGGacg                                                          >  1:3068280/1‑69 (MQ=255)
              gctgACTGGTACAACTCCAGCTACATCATCGCCTGGGGGTCAAACGTGCCGCAGACGCGTACCCCGGAt                                                           >  1:1039279/1‑69 (MQ=255)
              gctgACTGGTACAACTCCAGCTACATCATCGCCTGGGGGTCAAACGTGCCGCAGACGCGTACCACGGAt                                                           >  1:2394206/1‑69 (MQ=255)
                    tGGTATAACTCCAGCTACATCATCGCCTGGGGGTCTAACGTACCGCAGACACGTACGCCGGACGCCCAct                                                    >  1:3605696/1‑70 (MQ=255)
                     ggTACAACTCCAGCTACATCATCGCCTGGGGGGCAAACGTGCCGCAGACGCGTACCCCGGATGCTCAct                                                    <  1:350138/69‑1 (MQ=255)
                      gTATAACTCCAGCTACATCATCGCCTGGGGGTCTAACGTACCGCAGACACGTACGCCGGACGCCCActtct                                                 >  1:3538926/1‑71 (MQ=255)
                      gTACAACTCCAGCTACATCATCGCCTGGGGGTCAAACGTGCCGCAGACGCGTACCCCGGATGCTCActt                                                   <  1:1521/69‑1 (MQ=255)
                       tACAACTCCAGCTACATCATCGCCTGGGGGTCAAACGTGCCGCAGACGCGTAcccc                                                               <  1:5281022/56‑1 (MQ=255)
                       tACAACTCCAGCTACATCATCGCCTGGGGGTCAAACGTGCCGCAGACGCGTAcccc                                                               <  1:853902/56‑1 (MQ=255)
                       tACAACTCCAGCTACATCATCGCCTGGGGGTCAAACGTGCCGCAGACGCGTACCCCGGATGCTCActtctt                                                <  1:2389662/71‑1 (MQ=255)
                        aCAACTCCAGCTACATCATCGCCTGGGGGTCAAACGTGCCGCAGACGCGTACCCCGGATGCTCActtctt                                                >  1:5534822/1‑70 (MQ=255)
                         taaCTCCAGCTACATCATCGCCTGGGGGTCTAACGTACCGCAGACACGTACGCCGGACGCCCACTTCttt                                               <  1:1688819/69‑1 (MQ=255)
                         taaCTCCAGCTACATCATCGCCTGGGGGTCTAACGTACCGCAGACACGTACGCCGGACGCCCACTTCttt                                               <  1:4595201/69‑1 (MQ=255)
                         taaCTCCAGCTACATCATCGCCTGGGGGTCTAACGTACCGCAGACACGTACGCCGGACGCCCACTTCTTTa                                              >  1:5046981/2‑71 (MQ=255)
                          aaCTCCAGCTACATCATCGCCTGGGGGTCAAACGTGCCGCAGACGCGTACCCCGGATGCt                                                        <  1:4730690/60‑1 (MQ=255)
                          aaCTCCAGCTACATCATCGCCTGGGGGTCAAACGTGCCGCAGACGCGTACCCCGGATGCt                                                        <  1:2662608/60‑1 (MQ=255)
                           aCTCCAGCTACATCATCGCCTGGGGGTCTAACGTACCTCAGACACGTACGCCGGACGCCCACTTCTTTAcc                                            >  1:3817375/1‑70 (MQ=255)
                             tCCAGCTACATCATCGCCTGGGGGTCTAACGTACCGCAGACACGTACGCCGGACGCCCActt                                                   <  1:1938902/62‑1 (MQ=255)
                             tCCAGCTACATCATCGCCTGGGGGTCTAACGTACCGCAGACACGTACGCCGGACGCCCACTTCTTTAccg                                           <  1:2584830/70‑3 (MQ=255)
                              ccAGCTACATCATCGCCTGGGGGTCTAACGTACCGCAGACACGTACGCCGGa                                                            >  1:3316330/1‑52 (MQ=255)
                              ccAGCTACATCATCGCCTGGGGGTCAAACGTGCCGCAGACGCGTACCCCGGAt                                                           >  1:1726886/1‑53 (MQ=255)
                               cAGCTACATCATCGCCTGGGGGTCTAACGTACCGCAGACACGTACGCCGGACGCCCACTTCTTTACCGa                                          <  1:4799217/69‑1 (MQ=255)
                               cAGCTACATCATCGCCTGGGGGTCTAACGTACCGCAGACACGTACGCCGGACGCCCACTTCTTTACCGa                                          <  1:650272/69‑1 (MQ=255)
                                aGCTACATCATCGCCTGGGGGTCTAACGTACCGCAGACACGTACGCCGGACGCCCACTTCTTTACCGAAGt                                       <  1:4962118/71‑1 (MQ=255)
                                 gCTACATCATCGCCTGGGGGTCTAACGTACCGCAGACACGTACGCCg                                                              <  1:2546545/47‑1 (MQ=255)
                                     cctcatcGCCTGGGGGTCAAACGTGCCGCAGACGCGTACCCCGGATGCTCACTTCTTTACTGAAGTGCGt                                   >  1:3551809/3‑70 (MQ=255)
                                     catcatCGCCTGGGGTTCAAACGTGCCGCAGACGCGTACCCCGGATGCTCActtc                                                  >  1:4994262/1‑55 (MQ=255)
                                     catcatCGCCTGGGGGTCTAACGTACCGCAGACACGTACGCCGGACGCCCACTTCTTTACCGAAGTACgc                                   <  1:4611402/70‑2 (MQ=255)
                                     catcatCGCCTGGGGGTCAAACGTGCCGCAGACGCGTACCCCGGATGCTCACTTCTTTACTGAAGTGCGt                                   >  1:2484509/1‑70 (MQ=255)
                                      atcatcGCCTGGGGGTCTATCGTACCGCAGACACGTACGCCGGACGCCCActt                                                   <  1:134433/53‑1 (MQ=255)
                                      atcatcGCCTGGGGGTCTAACGTACCGCAGACACGTACGCCGGACGCCCACTTCTTTACCGAAGTACGCTa                                 >  1:656725/1‑71 (MQ=255)
                                       tcatcGCCTGGGGGTCAAACGTGCCGCAGACGCGTACCCCGGATGCTCACTTCTTTa                                              >  1:2728192/1‑57 (MQ=255)
                                        catcGCCTGGGGGTCTAACGTACCGCAGACACGTACGCCGGACGCCCACTTCTTTACCGAAGTACGCTAc                                >  1:5535609/1‑70 (MQ=255)
                                        catcGCCTGGGGGTCTAACGTACCGCAGACACGTACGCCGGACGCCCACTTCTTTACCGAAGTACGCTAc                                >  1:4222716/1‑70 (MQ=255)
                                         atcGCCTGGGGGTCTAACGTACCGCAGACACGTACGCCGGACGCCCACTTCTTTACCGAAGTACGCTACa                               >  1:4172383/1‑70 (MQ=255)
                                         atcGCCTGGGGGTCAAACGTGCCGCAGACGCGTACCCCGGATGCTCACTTCTTTACTGAAGTGCGTTACaa                              <  1:2475442/71‑1 (MQ=255)
                                         atcGCCTGGGGGTCAAACGTGCCGCAGACGCGTACCCCGGATGCTCACTTCTTTACTGAAGTGCGTTACa                               >  1:3839864/1‑70 (MQ=255)
                                         atcGCCTGGGGGTCAAACGTGCCGCAGACGCGTACCCCGGATGCTCACTTCTTTACTGAAGTGCGTTACa                               >  1:2794444/1‑70 (MQ=255)
                                         atcGCCTGGGGGTCAAACGTGCCGCAGACGCGTACCCCGGATGCTCACTTCTTTACTGAAGTGCGTTACa                               >  1:1620070/1‑70 (MQ=255)
                                          tcGCCTGGGGGTCTAACGTACCGCAGACACGTACGCCGGACGCCCACTTCTTTAccg                                           <  1:812926/57‑3 (MQ=255)
                                          tcGCCTGGGGGTCTAACGTACCGCAGACACGTACGCCGGACGCCCACTTCTTTAccg                                           <  1:3721680/57‑3 (MQ=255)
                                          tcGCCTGGGGGTCTAACGTACCGCAGACACGTACGCCGGACGCCCACTTCTTTACAGAAGTACGCTACaaa                             >  1:2735956/1‑71 (MQ=255)
                                          tcGCCTGGGGGTCAAACGTGCCGCAGACGCGTACCCCGGATGCTCActtc                                                  <  1:2392652/50‑1 (MQ=255)
                                          tcGCCTGGGGGTCAAACGTGCCGCAGACGCGTACCCCGGATGCTCACTTCTTTACTGAAGTGCGTTACaaa                             <  1:3325938/71‑1 (MQ=255)
                                           cGCCTGGGGGTCTAACGTACCGCAGACACGTACGCCGGACGCCCACTTCTTTACCGAAGTACGCTACAAAg                            >  1:1353362/1‑71 (MQ=255)
                                            gCCTGGGGGTCAAACGTGCCGCAGACGCGTACCCCGGATGCTCACTTCTTTACTGAAGTGCGTTACAAAg                            <  1:5040542/70‑1 (MQ=255)
                                            gCCTGGGGGTCAAACGTGCCGCAGACGCGTACCCCGGATGCTCACTTCTTTACTGAAGTGCGTTACAAAg                            <  1:2757397/70‑1 (MQ=255)
                                                 ggggTCTAACGTACCGCAGACACGTACGCCGGACGCCCACTTCTTTACCGAAGTACGCTACAAAGGCActa                      <  1:3623406/71‑3 (MQ=255)
                                                 ggggTCTAACGTACCGCAGACACGTACGCCGGACGCCCACTTCTTTACCGAAGTACGCTACAAAGGCActa                      <  1:2941623/71‑3 (MQ=255)
                                                  gggTCTAACGTACCGCAGACACGTACGCCGGACGCCCACTTCTTTACCGAAGTACGCTACAAAGGCACTaa                     <  1:5529506/71‑1 (MQ=255)
                                                  gggTCAAACGTGCCGCAGACGCGTACCCCGGATGCTCAc                                                     >  1:4414876/1‑39 (MQ=255)
                                                  gggTCAAACGTGCCGCAGACGCGTACCCCGGATGCTCACTTCTTTACTGAAGTGCGTTACAAAGGGACCaa                     <  1:1378252/71‑1 (MQ=255)
                                                  gggTCAAACGTGCCGCAGACGCGTACCCCGGATGCTCACTTCTTTACTGAAGTGCGTTACAAAGGGACCaa                     <  1:3847510/71‑1 (MQ=255)
                                                  gggTCAAACGTGCCGCAGACGCGTACCCCGGATGCTCACTTCTTTACTGAAGTGCGTTACAAAGGGACCaa                     <  1:243501/71‑1 (MQ=255)
                                                   ggTCAAACGTGCCGCAGACGCGTACCCCGGATGCTCACTTCTTTACTGAAGTGCGTTACAAAGGGACCaaa                    <  1:2029313/71‑1 (MQ=255)
                                                     tctaaCGTACCGCAGACACGTACGCCGGACGCCCACTTCTTTACCGAAGTACGCTACAAAGGCACTAAAAc                  <  1:5613126/68‑1 (MQ=255)
                                                      cAAACGTGCCGCAGACGCGTACCCCGGATGCTCACTTCTTTACTGAAGTGCGTTACAAAgg                           >  1:113967/1‑61 (MQ=255)
                                                       aaaCGTGCCGCAGACGCGTACCCCGGATGCTCActtctt                                                <  1:3573448/39‑1 (MQ=255)
                                                       aaaCGTGCCGCAGACGCGTACCCCGGATGCTCActtctt                                                <  1:5332486/39‑1 (MQ=255)
                                                       aaaCGTGCCGCAGACGCGTACCCCGGATGCTCACTTCTTTACTGaa                                         >  1:1881890/1‑46 (MQ=255)
                                                       aaaCGTGCCGCAGACGCGTACCCCGGATGCTCACTTCTTTACTGAAGTGCGTTACAAAgg                           <  1:3776140/60‑1 (MQ=255)
                                                       aaaCGTGCCGCAGACGCGTACCCCGGATGCTCACTTCTTTACTGAAGTGCGTTACAAAGGGACCAAAACTg                >  1:3052503/1‑71 (MQ=255)
                                                        aaCGTGCCGCAGACGCGTACCCCGGATGCTCACTTCTTTACTGAAGTGCGTTACAAAGGGACCaaa                    <  1:1482629/66‑1 (MQ=255)
                                                         aCGTGCCGCAGACGCGTACCCCGGATGCTCACTTCTTTACTGAAGTGCGTTACAAAGGGACCAAAACTGtc              <  1:3143133/71‑2 (MQ=255)
                                                         aCGTGCCGCAGACGCGTACCCCGGATGCTCACTTCTTTACTGAAGTGCGTTACAAAGGGACCAAAACTGt               <  1:164303/70‑1 (MQ=255)
                                                         aCGTACCGCAGACACGTACGCCGGACGCCCACTTCTTTACCGAAg                                        >  1:464371/1‑45 (MQ=255)
                                                         aCGTACCGCAGACACGTACGCCGGACGCCCACTTCTTTACCGAAg                                        >  1:2466735/1‑45 (MQ=255)
                                                         aCGTACCGCAGACACGTACGCCGGACGCCCACTTCTTTACCGAAGTACGCTACAAAGGCACTAAAAc                  >  1:1477693/1‑67 (MQ=255)
                                                          cGTGCCGCAGACGCGTACCCCGGATGCTCActtctt                                                <  1:3762885/36‑1 (MQ=255)
                                                          cGTGCCGCAGACGCGTACCCCGGATGCTCACTTCTTTACTGAAGTGCGTTACAAAGGGACCAAAAc                  >  1:270907/1‑66 (MQ=255)
                                                          cGTGCCGCAGACGCGTACCCCGGATGCTCACTTCTTTACTGAAGTGCGTTACAAAGGGACCAAAACTGTTg             >  1:824326/1‑71 (MQ=255)
                                                           gTGCCGCAGACGCGTACCCCGGATGCTCACTTCTTTACTGAAGTGCGTTACAAAGGGACCAAAACTGTTg             >  1:1725713/1‑70 (MQ=255)
                                                           gTGCCGCAGACGCGTACCCCGGATGCTCACTTCTTTACTGAAGTGCGTTACAAAGGGACCAAAACTGTTg             >  1:2942999/1‑70 (MQ=255)
                                                           gTGCCGCAGACGCGTACCCCGGATGCTCACTTCTTTACTGAAGTGCGTTACAAAGGGACCAAAACTGTTGc            >  1:654801/1‑71 (MQ=255)
                                                           gTGCCGCAGACGCGTACCCCGGATGCTCACTTCTTTACTGAAGTGCGTTACAAAGGGACCAAAACTGTTGc            >  1:2328699/1‑71 (MQ=255)
                                                            tGCCGCAGACGCGTACCCCGGATGCTCACTTCtttt                                              >  1:3518208/1‑35 (MQ=255)
                                                            tGCCGCAGACGCGTACCCCGGATGCTCACTTCTTTa                                              >  1:4410367/1‑36 (MQ=255)
                                                            tGCCGCAGACGCGTACCCCGGATGCTCACTTCTTTACTGAAGTGCGTTACAAAGGGACCAAAACTGTTGcc           >  1:350784/1‑71 (MQ=255)
                                                             gCCGCAGACGCGTACCCCGGATGCTCACTTCTTTACTGAAGTGCGTTACAAAGGGACCAAAACTGTTGCCg          >  1:2668483/1‑71 (MQ=255)
                                                              ccGCAGACGCGTACCCCGGATGCTCACTTCTTTACTGAAGTGCGTTACAAAGGGACCAAAACTGTTGCCGt         <  1:5044771/71‑1 (MQ=255)
                                                              ccGCAGACGCGTACCCCGGATGCTCACTTCTTTACTGAAGTGCGTTACAAAGGGACCAAAACTGTTGCCGt         <  1:2411531/71‑1 (MQ=255)
                                                                  aGACGCGTACCCCGGATGCTCACTTCTTTACTGAAGTGCGTTACaaa                             >  1:5423738/1‑47 (MQ=255)
                                                                     cgcgTACCCCGGATGCTCACTTCTTTACTGAAGTGCGTTACAAAGGGACCAAAACTGTTGCCGTCACACCa  <  1:568557/71‑1 (MQ=255)
                                                                      gcgTACCCCGGATGCTCACTTCTTTACTGAAGTGCGTTACAAAGGGACCAAAACTGTTGCCGTCacac    >  1:4665990/1‑68 (MQ=255)
                                                                      |                                                                     
ACGTACCGGAATCTGCTGACTGGTACAACTCCAGCTACATCATCGCCTGGGGGTCAAACGTGCCGCAGACGCGTACCCCGGATGCTCACTTCTTTACTGAAGTGCGTTACAAAGGGACCAAAACTGTTGCCGTCACACCA  >  minE/832252‑832391

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