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 832,307 A→T 49.0% S255S (TCA→TCT)  narG → nitrate reductase 1, alpha subunit

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE832,3070AT49.0% 2.6 / 154.6 102S255S (TCA→TCT) narGnitrate reductase 1, alpha subunit
Reads supporting (aligned to +/- strand):  ref base A (29/23);  new base T (19/31);  total (48/54)
Fisher's exact test for biased strand distribution p-value = 7.87e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

Only 100 of 117 total aligned reads displayed.

GGGCGAGCAAACTGACGTACCGGAATCTGCTGACTGGTACAACTCCAGCTACATCATCGCCTGGGGGTCAAACGTGCCGCAGACGCGTACCCCGGATGCTCACTTCTTTACTGAAGTGCGTTACAAAGGGACCAAAACTG  >  minE/832238‑832377
                                                                     |                                                                      
gggCGAGCAAACTGACGTACCGGAATCTGCTGACTGGTACAACTCCAGCTACATCATCGCCTGGGGGTCa                                                                        >  1:2219594/1‑70 (MQ=255)
    gAGCAAACCGACGTACCGGAATCTGCCGACTGGTATAACTCCAGCTACATCATCGCCTGGGGGTCTAACGt                                                                   <  1:4493414/71‑1 (MQ=255)
      gCAAACTGACGTACCGGAATCTGCTGACTGGTACAACTCCAGCTACATCATCGCCTGGGGGTCAAACGTGc                                                                 <  1:383673/71‑1 (MQ=255)
      gCAAACCGACGTACCGGAATCTGCCGACTGGTATAACTCCAGCTACATCATCGCCTGGGGGTCTAACGtac                                                                 <  1:120337/71‑3 (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)
            tGACGTACCGGAATCTGCTGACTGGTACAACTCCAGCTACATCATCGCCTGGGGGTCAAACg                                                                    >  1:3295964/1‑62 (MQ=255)
            tGACGTACCGGAATCTGCTGACTGGTACAACTCCAGCTACATCATCGCCTGGGGGTCAAACg                                                                    >  1:170113/1‑62 (MQ=255)
            cgACGTACCGGAATCTGCCGACTGGTATAACTCCAGCTACATCATCGCCTGGGGGTCTAACGTACCGCAGa                                                           >  1:1384451/2‑71 (MQ=255)
             gACGTACCGGAATCTGCCGACTGGTATAACTCCAGCTACATCATCGCCTGGGGGTCTAACGTACCGCAGa                                                           >  1:5269461/1‑70 (MQ=255)
             gACGTACCGGAATCTGCCGACTGGTATAACTCCAGCTACATCATCGCCTGGGGGTCTAACGTACCGCAGa                                                           >  1:781607/1‑70 (MQ=255)
             gACGTACCGGAATCTGCCGACTGGTATAACTCCAGCTACATCATCGCCTGGGGGTCTAACGTACCGCAGa                                                           >  1:1956245/1‑70 (MQ=255)
             gACGTACCGGAATCTGCCGACTGGTATAACTCCAGCTACATCATCGCCTGGGGGTCTAACGTACCGCAGAc                                                          <  1:4100523/71‑1 (MQ=255)
              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)
                    cGGAATCTGCCGACTGGTATAACTCCAGCTACATCATCGCCTGGGGGTCTAACGTACCg                                                               <  1:1970589/59‑1 (MQ=38)
                      gAATCTGCTGACTGGTACAACTCCAGCTACATCATCGCCTGGGGGTCAAACGTGCCGCAGACGCGTAcccc                                                 >  1:2135068/1‑71 (MQ=255)
                      gAATCTGCTGACTGGTACAACTCCAGCTACATCATCGCCTGGGGGTCAAACGTGCCGCAGACGCGTAcc                                                   >  1:3576965/1‑69 (MQ=255)
                      gAATCTGCCGACTGGTATAACTCCAGCTACATCATCGCCTGGGGGTCtaa                                                                      >  1:2442026/1‑50 (MQ=38)
                      gAATCTGCCGACTGGTATAACTCCAGCTACATCATCGCCTGGGGGTCTAACGTACCGCAGACACGTAcgcc                                                 <  1:878330/71‑1 (MQ=255)
                      gAATCTGCCGACTGGTATAACTCCAGCTACATCATCGCCTGGGGGTCTAACGTACCGCAGACACGTAcgcc                                                 <  1:935558/71‑1 (MQ=255)
                       aaTCTGCTGACTGGTACAACTCCAGCTACATCATCGCCTGGGGGTCAAACGTGCCGCAGACGCGt                                                      <  1:2089654/65‑1 (MQ=255)
                       aaTCTGCTGACTGGTACAACTCCAGCTACATCATCGCCTGGGGGTCAAACGTGCCGCAGACGCGt                                                      <  1:5454331/65‑1 (MQ=255)
                        aTCTGCTGACTGGTACAACTCCAGCTACATCATCGCCTGGGGGTCAAACGTGCCGCAGACGCGTACCCCgg                                               <  1:3040704/71‑1 (MQ=255)
                         tCTGCTGACTGGTACAACTCCAGCTACATCATCGCCTGGGGGTCaa                                                                       <  1:519489/46‑1 (MQ=255)
                         tCTGCTGACTGGTACAACTCCAGCTACATCATCGCCTGGGGGTCaa                                                                       <  1:2711814/46‑1 (MQ=255)
                         tCTGCTGACTGGTACAACTCCAGCTACATCATCGCCTGGGGGTCAAACGTGCCGCAGACGCGTAc                                                    >  1:127842/1‑65 (MQ=255)
                         tCTGCTGACTGGTACAACTCCAGCTACATCATCGCCTGGGGGTCAAACGTGCCGCAGACGCGTAc                                                    >  1:166102/1‑65 (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)
                              tgACTGGTACAACTCCAGCTACATCATCGCCTGGGGGTCaa                                                                       <  1:5640793/41‑1 (MQ=255)
                              tgACTGGTACAACTCCAGCTACATCATCGCCTGGGGGTCaa                                                                       <  1:2425721/41‑1 (MQ=255)
                                aCTGGTACAACTCCAGCTACATCATCGCCTGGGGGTCAAAc                                                                     >  1:1631243/1‑41 (MQ=255)
                                  tGGTATAACTCCAGCTACATCATCGCCTGGGGGTCTAACGTACCGCAGACACGTACGCCGGACGCCCAct                                      >  1:3605696/1‑70 (MQ=255)
                                   ggTATAACTCCAGCTACATCATCGCCTGGGGGTCTAACGTACCg                                                               >  1:1345933/1‑44 (MQ=255)
                                    gTATAACTCCAGTTACATCATCGCCTGGGGGTCTAACGta                                                                  <  1:4514718/40‑2 (MQ=37)
                                    gTATAACTCCAGTTACATCATCGCCTGGGGGTCTAACGta                                                                  <  1:429448/40‑2 (MQ=37)
                                    gTATAACTCCAGTTACATCATCGCCTGGGGGTCTAACGta                                                                  <  1:422803/40‑2 (MQ=37)
                                    gTATAACTCCAGCTACATCATCGCCTGGGGGTCTAACGTACCGCAGACACGTACGCCGGACGCCCActtct                                   >  1:3538926/1‑71 (MQ=255)
                                    gTATAACTCCAGCTACATCATCGCCTGGGGGTCTAACGTACCGCAGACACGTACGCCGGACGCCCActtc                                    <  1:3426758/70‑1 (MQ=255)
                                    gTACAACTCCAGCTACATCATCGCCTGGGGGTCAAACGTGCCGCa                                                             <  1:2813539/45‑1 (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                                 <  1:4595201/69‑1 (MQ=255)
                                        aaCTCCAGCTACATCATCGCCTGGGGGTCAAACGTGCCGCAGACGCGTACCCCGGATGCt                                          <  1:4730690/60‑1 (MQ=255)
                                        aaCTCCAGCTACATCATCGCCTGGGGGTCAAACGTGCCGCAGACGCGTACCCCGGATGCt                                          <  1:2662608/60‑1 (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                            <  1:650272/69‑1 (MQ=255)
                                             cAGCTACATCATCGCCTGGGGGTCTAACGTACCGCAGACACGTACGCCGGACGCCCACTTCTTTACCGa                            <  1:4799217/69‑1 (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)
                                                      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                 >  1:2794444/1‑70 (MQ=255)
                                                       atcGCCTGGGGGTCAAACGTGCCGCAGACGCGTACCCCGGATGCTCACTTCTTTACTGAAGTGCGTTACa                 >  1:1620070/1‑70 (MQ=255)
                                                       atcGCCTGGGGGTCAAACGTGCCGCAGACGCGTACCCCGGATGCTCACTTCTTTACTGAAGTGCGTTACa                 >  1:3839864/1‑70 (MQ=255)
                                                        tcGCCTGGGGGTCTAACGTACCGCAGACACGTACGCCGGACGCCCACTTCTTTAccg                             <  1:812926/57‑3 (MQ=255)
                                                        tcGCCTGGGGGTCTAACGTACCGCAGACACGTACGCCGGACGCCCACTTCTTTACAGAAGTACGCTACaaa               >  1:2735956/1‑71 (MQ=255)
                                                        tcGCCTGGGGGTCAAACGTGCCGCAGACGCGTACCCCGGATGCTCActtc                                    <  1:2392652/50‑1 (MQ=255)
                                                        tcGCCTGGGGGTCAAACGTGCCGCAGACGCGTACCCCGGATGCTCACTTCTTTACTGAAGTGCGTTACaaa               <  1:3325938/71‑1 (MQ=255)
                                                          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       <  1:3847510/71‑1 (MQ=255)
                                                                gggTCAAACGTGCCGCAGACGCGTACCCCGGATGCTCACTTCTTTACTGAAGTGCGTTACAAAGGGACCaa       <  1:243501/71‑1 (MQ=255)
                                                                gggTCAAACGTGCCGCAGACGCGTACCCCGGATGCTCACTTCTTTACTGAAGTGCGTTACAAAGGGACCaa       <  1:1378252/71‑1 (MQ=255)
                                                                 ggTCAAACGTGCCGCAGACGCGTACCCCGGATGCTCACTTCTTTACTGAAGTGCGTTACAAAGGGACCaaa      <  1:2029313/71‑1 (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)
                                                                     aaaCGTGCCGCAGACGCGTACCCCGGATGCTCACTTCTTTACTGAAGTGCGTTACAAAGGGACCAAAACTg  >  1:3052503/1‑71 (MQ=255)
                                                                     |                                                                      
GGGCGAGCAAACTGACGTACCGGAATCTGCTGACTGGTACAACTCCAGCTACATCATCGCCTGGGGGTCAAACGTGCCGCAGACGCGTACCCCGGATGCTCACTTCTTTACTGAAGTGCGTTACAAAGGGACCAAAACTG  >  minE/832238‑832377

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A