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 832,313 G→A 41.2% V257V (GTG→GTA)  narG → nitrate reductase 1, alpha subunit

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE832,3130GA41.2% 65.4 / 123.5 114V257V (GTG→GTA) narGnitrate reductase 1, alpha subunit
Reads supporting (aligned to +/- strand):  ref base G (37/30);  new base A (22/25);  total (59/55)
Fisher's exact test for biased strand distribution p-value = 4.47e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.47e-01

Only 100 of 115 total aligned reads displayed.

GCAAACTGACGTACCGGAATCTGCTGACTGGTACAACTCCAGCTACATCATCGCCTGGGGGTCAAACGTGCCGCAGACGCGTACCCCGGATGCTCACTTCTTTACTGAAGTGCGTTACAAAGGGACCAAAACTGTTGCCG  >  minE/832244‑832383
                                                                     |                                                                      
gCAAACTGACGTACCGGAATCTGCTGACTGGTACAACTCCAGCTACATCATCGCCTGGGGGTCAAACGTGc                                                                       <  1:383673/71‑1 (MQ=255)
   aaCTGACGTACTGGAATCTGCTGACTGGTACAACTCCAGCTACATCATCGCCTGGGGGTCAAACGTGCCg                                                                     >  1:2519185/1‑70 (MQ=255)
   aaCTGACGTACCGGAATCTGCTGACTGGTACAACTCCAGCTACATCATCGCCTGGGGGTCAAACGTGCCg                                                                     >  1:3401781/1‑70 (MQ=255)
    accgACGTACCGGAATCTGCCGACTGGTATAACTCCAGCTACATCATCGCCTGGGGGTCTAACGTACCg                                                                     >  1:468365/4‑69 (MQ=255)
    accgACGTACCGGAATCTGCCGACTGGTATAACTCCAGCTACATCATCGCCTGGGGGTCTAACGTACCGCa                                                                   <  1:5522420/68‑1 (MQ=255)
    aCTGACGTACCGGAATCTGCTGACTGGTACAACTCCAGCTACATCATCGCCTGGGGGTCAAACGTGCCGCa                                                                   <  1:2961473/71‑1 (MQ=255)
       gACGTACCGGAATCTGCCGACTGGTATAACTCCAGCTACATCATCGCCTGGGGGTCTAACGTACCGCAGa                                                                 >  1:781607/1‑70 (MQ=255)
       gACGTACCGGAATCTGCCGACTGGTATAACTCCAGCTACATCATCGCCTGGGGGTCTAACGTACCGCAGa                                                                 >  1:1956245/1‑70 (MQ=255)
       gACGTACCGGAATCTGCCGACTGGTATAACTCCAGCTACATCATCGCCTGGGGGTCTAACGTACCGCAGa                                                                 >  1:5269461/1‑70 (MQ=255)
       gACGTACCGGAATCTGCCGACTGGTATAACTCCAGCTACATCATCGCCTGGGGGTCTAACGTACCGCAGAc                                                                <  1:4100523/71‑1 (MQ=255)
        aCGTACCGGAATCTGCTGACTGGTACAACTCCAGCTACATCATCGCCTGGGGGTCAAACGTGCCGCAGAcg                                                               >  1:2852621/1‑71 (MQ=255)
            aCCGGAATCTGCCGACTGGTATAACTCCAGCTACATCATCGCCTGGGGGTCTAACGTACCg                                                                     <  1:3213199/61‑1 (MQ=255)
             ccGGAATCTGCCGACTGGTATAACTCCAGCTACATCATCGCCTGGGGGTCTAACGTACCGCAGACACGTAc                                                          >  1:2828340/1‑71 (MQ=255)
              cGGAATCTGCTGACTGGTACAACTCCAGCTACATCATCGCCTGGGGGTCAAACGTGCCGCAGAcgcg                                                             <  1:3832576/67‑1 (MQ=255)
              cGGAATCTGCCGACTGGTATAACTCCAGCTACATCATCGCCTGGGGGTCTAACGTACCg                                                                     <  1:1970589/59‑1 (MQ=38)
               ggAATCTGCCGACTGGTATAACTCCAGCTACATCATCGCCTGGGGGTCTAACGTACCg                                                                     <  1:4413453/58‑1 (MQ=38)
                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                                                            <  1:2089654/65‑1 (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)
                             ggTATAACTCCAGCTACATCATCGCCTGGGGGTCTAACGTACCg                                                                     >  1:1345933/1‑44 (MQ=255)
                              gTATAACTCCAGCTACATCATCGCCTGGGGGTCTAACGTACCGCAGACACGTACGCCGGACGCCCActtct                                         >  1:3538926/1‑71 (MQ=255)
                              gTATAACTCCAGCTACATCATCGCCTGGGGGTCTAACGTACCGCAGACACGTACGCCGGACGCCCActtc                                          <  1:3426758/70‑1 (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)
                                  aaCTCCAGCTACATCATCGCCTGGGGGTCTAACGTACCGCAg                                                                  <  1:2017198/42‑1 (MQ=255)
                                  aaCTCCAGCTACATCATCGCCTGGGGGTCAAACGTGCCGCAGACGCGTACCCCGGATGCt                                                <  1:2662608/60‑1 (MQ=255)
                                  aaCTCCAGCTACATCATCGCCTGGGGGTCAAACGTGCCGCAGACGCGTACCCCGGATGCt                                                <  1:4730690/60‑1 (MQ=255)
                                   aCTCCAGCTACATCATCGCCTGGGGGTCTAACGTACCTCAGACACGTACGCCGGACGCCCACTTCTTTAcc                                    >  1:3817375/1‑70 (MQ=255)
                                    cTCCAGCTACATCATCGCCTGGGGGTCAAACGTGCCGc                                                                    >  1:2948096/1‑38 (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)
                                               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                       >  1:1620070/1‑70 (MQ=255)
                                                 atcGCCTGGGGGTCAAACGTGCCGCAGACGCGTACCCCGGATGCTCACTTCTTTACTGAAGTGCGTTACa                       >  1:2794444/1‑70 (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              <  1:2941623/71‑3 (MQ=255)
                                                         ggggTCTAACGTACCGCAGACACGTACGCCGGACGCCCACTTCTTTACCGAAGTACGCTACAAAGGCActa              <  1:3623406/71‑3 (MQ=255)
                                                          gggTCTAACGTACCGCAGACACGTACGCCGGACGCCCACTTCTTTACCGAAGTACGCTACAAAGGCACTaa             <  1:5529506/71‑1 (MQ=255)
                                                          gggTCAAACGTGCCGCAGACGCGTACCCCGGATGCTCACTTCTTTACTGAAGTGCGTTACAAAGGGACCaa             <  1:3847510/71‑1 (MQ=255)
                                                          gggTCAAACGTGCCGCAGACGCGTACCCCGGATGCTCACTTCTTTACTGAAGTGCGTTACAAAGGGACCaa             <  1:1378252/71‑1 (MQ=255)
                                                             tctaaCGTACCGCAGACACGTACGCCGGACGCCCACTTCTTTACCGAAGTACGCTACAAAGGCACTAAAAc          <  1:5613126/68‑1 (MQ=255)
                                                              cAAACGTGCCGCAGACGCGTACCCCGGATGCTCACTTCTTTACTGAAGTGCGTTACAAAgg                   >  1:113967/1‑61 (MQ=255)
                                                               aaaCGTGCCGCAGACGCGTACCCCGGATGCTCActtctt                                        <  1:5332486/39‑1 (MQ=255)
                                                               aaaCGTGCCGCAGACGCGTACCCCGGATGCTCActtctt                                        <  1:3573448/39‑1 (MQ=255)
                                                               aaaCGTGCCGCAGACGCGTACCCCGGATGCTCACTTCTTTACTGaa                                 >  1:1881890/1‑46 (MQ=255)
                                                               aaaCGTGCCGCAGACGCGTACCCCGGATGCTCACTTCTTTACTGAAGTGCGTTACAAAgg                   <  1:3776140/60‑1 (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     >  1:2942999/1‑70 (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)
                                                                     |                                                                      
GCAAACTGACGTACCGGAATCTGCTGACTGGTACAACTCCAGCTACATCATCGCCTGGGGGTCAAACGTGCCGCAGACGCGTACCCCGGATGCTCACTTCTTTACTGAAGTGCGTTACAAAGGGACCAAAACTGTTGCCG  >  minE/832244‑832383

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